@article{Shapovalov2025,
  author = "I. Shapovalov and P. Rimal and P. Poudel and V. Lewtas and M. Bell and S. K. Panday and B. J. Laight and D. Harper and S. Grieve and G. S. Baillie and K. Nouri and P. L. Davies and E. Alexov and P. A. Greer",
  title = "Quantification and structure-function analysis of calpain-1 and calpain-2 protease subunit interactions",
  year = 2025,
  journal = "Journal of Biological Chemistry",
  publisher = "Elsevier BV",
  pages = "110243",
  month = "May",
  doi = "10.1016/j.jbc.2025.110243",
  url = "http://dx.doi.org/10.1016/j.jbc.2025.110243"
}


@article{Poudel2025,
  author = "P. Poudel and I. Shapovalov and S. K. Panday and K. Nouri and P. L. Davies and P. A. Greer and E. Alexov",
  title = "In Silico Screening for Small Molecules to Alter Calpain Proteolysis through Modulating Conformation Changes Induced by Heterodimerization",
  year = 2025,
  journal = "Journal of Chemical Information and Modeling",
  publisher = "American Chemical Society (ACS)",
  month = "May",
  doi = "10.1021/acs.jcim.5c00258",
  url = "http://dx.doi.org/10.1021/acs.jcim.5c00258"
}


@article{Chen2025,
  author = "A. Y. Chen and S. K. Panday and K. Ri and E. Alexov and B. R. Brooks and A. Damjanovic",
  title = "PKAD-R: Curated, Redesigned and Expanded Database of Experimental pKa Values in Proteins",
  year = 2025,
  journal = "Journal of Computational Biophysics and Chemistry",
  publisher = "World Scientific Pub Co Pte Ltd",
  pages = "1–15",
  month = "Apr",
  doi = "10.1142/s2737416525500164",
  url = "http://dx.doi.org/10.1142/S2737416525500164"
}


@article{Poudel2025,
  author = "P. Poudel and M. A. Miteva and E. Alexov",
  title = "Strategies for in Silico Drug Discovery to Modulate Macromolecular Interactions Altered by Mutations",
  year = 2025,
  journal = "Frontiers in Bioscience-Landmark",
  publisher = "IMR Press",
  volume = 30,
  number = 4,
  month = "Apr",
  doi = "10.31083/fbl26339",
  url = "http://dx.doi.org/10.31083/FBL26339"
}


@article{Turina2025,
  author = "P. Turina and M. Petrosino and C. A. E. Sandoval and L. Novak and A. Pasquo and E. Alexov and M. A. Alladin and D. B. Ascher and G. Babbi and C. Bakolitsa and R. Casadio and J. Cheng and P. Fariselli and L. Folkman and A. Kamandula and P. Katsonis and M. Li and D. Li and O. Lichtarge and S. Mahmud and P. L. Martelli and D. Pal and S. K. Panday and D. E. V. Pires and S. Portelli and F. Pucci and C. H. M. Rodrigues and M. Rooman and C. Savojardo and M. Schwersensky and Y. Shen and A. V. Strokach and Y. Sun and J. Woo and P. Radivojac and S. E. Brenner and R. Chiaraluce and V. Consalvi and E. Capriotti",
  title = "Assessing the predicted impact of single amino acid substitutions in MAPK proteins for CAGI6 challenges",
  year = 2025,
  journal = "Human Genetics",
  publisher = "Springer Science and Business Media LLC",
  volume = 144,
  number = 23,
  pages = "265–280",
  month = "Feb",
  doi = "10.1007/s00439-024-02724-8",
  url = "http://dx.doi.org/10.1007/s00439-024-02724-8"
}


@article{Rimal2025,
  author = "P. Rimal and S. Paul and S. Panday and E. Alexov",
  title = "Further Development of SAMPDI-3D: A Machine Learning Method for Predicting Binding Free Energy Changes Caused by Mutations in Either Protein or DNA",
  year = 2025,
  journal = "Genes",
  publisher = "MDPI AG",
  volume = 16,
  number = 1,
  pages = "101",
  month = "Jan",
  doi = "10.3390/genes16010101",
  url = "http://dx.doi.org/10.3390/genes16010101"
}


@book{alexov2025approaches,
  author = "E. Alexov",
  title = "Approaches Of Computational Biophysics And Chemistry In Molecular Biology",
  year = 2025,
  publisher = "World Scientific"
}


@article{koirala2025dynamics,
  author = "M. Koirala and E. Alexov",
  title = "Dynamics (DFMD) Approach",
  year = 2025,
  journal = "Approaches Of Computational Biophysics And Chemistry In Molecular Biology",
  publisher = "World Scientific",
  pages = "79"
}


@article{Turina2024,
  author = "P. Turina and G. D. Cortivo and C. A. E. Sandoval and E. Alexov and D. B. Ascher and G. Babbi and C. Bakolitsa and R. Casadio and P. Fariselli and L. Folkman and A. Kamandula and P. Katsonis and D. Li and O. Lichtarge and P. L. Martelli and S. K. Panday and D. E. V. Pires and S. Portelli and F. Pucci and C. H. M. Rodrigues and M. Rooman and C. Savojardo and M. Schwersensky and Y. Shen and A. V. Strokach and Y. Sun and J. Woo and P. Radivojac and S. E. Brenner and D. Dell’Orco and E. Capriotti",
  title = "Assessing the predicted impact of single amino acid substitutions in calmodulin for CAGI6 challenges",
  year = 2024,
  journal = "Human Genetics",
  publisher = "Springer Science and Business Media LLC",
  volume = 144,
  number = 23,
  pages = "113–125",
  month = "Dec",
  doi = "10.1007/s00439-024-02720-y",
  url = "http://dx.doi.org/10.1007/s00439-024-02720-y"
}


@article{Panday2024,
  author = "S. K. Panday and V. Shankar and R. A. Lyman and E. Alexov",
  title = "Genetic Variants Linked to Opioid Addiction: A Genome-Wide Association Study",
  year = 2024,
  journal = "International Journal of Molecular Sciences",
  publisher = "MDPI AG",
  volume = 25,
  number = 23,
  pages = "12516",
  month = "Nov",
  doi = "10.3390/ijms252312516",
  url = "http://dx.doi.org/10.3390/ijms252312516"
}


@article{Panday2024,
  author = "S. K. Panday and A. Chakravorty and S. Zhao and E. Alexov",
  title = "On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super‐Gaussian Poisson–Boltzmann model",
  year = 2024,
  journal = "Journal of Computational Chemistry",
  publisher = "Wiley",
  volume = 46,
  number = 1,
  month = "Oct",
  doi = "10.1002/jcc.27496",
  url = "http://dx.doi.org/10.1002/jcc.27496"
}


@article{Rimal2024,
  author = "P. Rimal and S. K. Panday and W. Xu and Y. Peng and E. Alexov",
  title = "SAAMBE-MEM: a sequence-based method for predicting binding free energy change upon mutation in membrane protein–protein complexes",
  year = 2024,
  journal = "Bioinformatics",
  publisher = "Oxford University Press (OUP)",
  volume = 40,
  number = 9,
  month = "Sep",
  doi = "10.1093/bioinformatics/btae544",
  url = "http://dx.doi.org/10.1093/bioinformatics/btae544"
}


@article{Pandey2024,
  author = "P. Pandey and E. Alexov",
  title = "Most Monogenic Disorders Are Caused by Mutations Altering Protein Folding Free Energy",
  year = 2024,
  journal = "International Journal of Molecular Sciences",
  publisher = "MDPI AG",
  volume = 25,
  number = 4,
  pages = "1963",
  month = "Feb",
  doi = "10.3390/ijms25041963",
  url = "http://dx.doi.org/10.3390/ijms25041963"
}


@article{Goutam2024,
  author = "R. K. Goutam and K. McDowell and E. Alexov and W. J. Edenfield and H. Sanabria",
  title = "DNA binding affinity of pathogenic missense mutations in the ARID domain of ARID1A",
  year = 2024,
  journal = "Biophysical Journal",
  publisher = "Elsevier BV",
  volume = 123,
  number = 3,
  pages = "503a",
  month = "Feb",
  doi = "10.1016/j.bpj.2023.11.3037",
  url = "http://dx.doi.org/10.1016/j.bpj.2023.11.3037"
}


@article{Zhao2024,
  author = "S. Zhao and I. E. Ijaodoro and M. McGowan and E. Alexov",
  title = "Calculation of electrostatic free energy for the nonlinear Poisson-Boltzmann model based on the dimensionless potential",
  year = 2024,
  journal = "Journal of Computational Physics",
  publisher = "Elsevier BV",
  volume = 497,
  pages = "112634",
  month = "Jan",
  doi = "10.1016/j.jcp.2023.112634",
  url = "http://dx.doi.org/10.1016/j.jcp.2023.112634"
}


@article{Pandey2023,
  author = "P. Pandey and S. K. Panday and P. Rimal and N. Ancona and E. Alexov",
  title = "Predicting the Effect of Single Mutations on Protein Stability and Binding with Respect to Types of Mutations",
  year = 2023,
  journal = "International Journal of Molecular Sciences",
  publisher = "MDPI AG",
  volume = 24,
  number = 15,
  pages = "12073",
  month = "Jul",
  doi = "10.3390/ijms241512073",
  url = "http://dx.doi.org/10.3390/ijms241512073"
}


@article{Pandey2023,
  author = "P. Pandey and S. Ghimire and B. Wu and E. Alexov",
  title = "On the linkage of thermodynamics and pathogenicity",
  year = 2023,
  journal = "Current Opinion in Structural Biology",
  publisher = "Elsevier BV",
  volume = 80,
  pages = "102572",
  month = "Jun",
  doi = "10.1016/j.sbi.2023.102572",
  url = "http://dx.doi.org/10.1016/j.sbi.2023.102572"
}


@article{Ancona2023,
  author = "N. Ancona and A. Bastola and E. Alexov",
  title = "PKAD-2: New Entries and Expansion of Functionalities of the Database of Experimentally Measured pKa’s of Proteins",
  year = 2023,
  journal = "Journal of Computational Biophysics and Chemistry",
  publisher = "World Scientific Pub Co Pte Ltd",
  volume = 22,
  number = 5,
  pages = "515–524",
  month = "Apr",
  doi = "10.1142/s2737416523500230",
  url = "http://dx.doi.org/10.1142/S2737416523500230"
}


@article{Goutam2023,
  author = "R. K. Goutam and E. Alexov and W. J. Edenfield and H. Sanabria",
  title = "Biophysical characterization of pathogenic missense mutation in the ARID domain of ARID1A",
  year = 2023,
  journal = "Biophysical Journal",
  publisher = "Elsevier BV",
  volume = 122,
  number = 3,
  pages = "330a",
  month = "Feb",
  doi = "10.1016/j.bpj.2022.11.1844",
  url = "http://dx.doi.org/10.1016/j.bpj.2022.11.1844"
}


@article{Shao2023a,
  author = "Y. Shao and M. McGowan and S. Wang and E. Alexov and S. Zhao",
  title = "Convergence of a diffuse interface Poisson-Boltzmann (pb) model to the sharp interface pb model: a unified regularization formulation",
  year = 2023,
  journal = "Applied Mathematics and Computation",
  volume = 436,
  pages = "127501"
}


@article{Sun2022a,
  author = "S. Sun and P. Poudel and E. Alexov and L. Li",
  title = "Electrostatics in Computational Biophysics and Its Implications for Disease Effects",
  year = 2022,
  journal = "International Journal of Molecular Sciences",
  volume = 23,
  number = 18,
  pages = "10347"
}


@article{Panday2022a,
  author = "S. Panday and E. Alexov",
  title = "Protein–Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation",
  year = 2022,
  journal = "ACS omega",
  volume = 7,
  number = 13,
  pages = "11057-11067"
}


@article{Wang2022a,
  author = "S. Wang and Y. Shao and E. Alexov and S. Zhao",
  title = "A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions",
  year = 2022,
  journal = "Journal of Computational Physics",
  pages = "111340"
}


@article{aprigliano2020increased,
  author = "R. Aprigliano and S. Bradamante and B. Mihaljevic and W. Wang and S. L. F. Martin and D. L. Bordin and M. Bosshard and N. P. Montaldo and Y. Peng and E. Alexov and others",
  title = "Increased p53 signaling impairs neural differentiation causing HUWE1-promoted intellectual disabilities",
  year = 2021,
  journal = "Cell Reports Medicine",
  publisher = "Cold Spring Harbor Laboratory",
  volume = 2,
  pages = "100240",
  month = "Apr",
  doi = "https://doi.org/10.1016/j.xcrm.2021.100240",
  url = "https://www.cell.com/cell-reports-medicine/pdf/S2666-3791(21)00056-2.pdf"
}


@article{koirala2021computational,
  author = "M. Koirala and H. Shashikala and J. Jeffries and B. Wu and S. K. Loftus and J. H. Zippin and E. Alexov",
  title = "Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease",
  year = 2021,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 22,
  number = 15,
  pages = "8273"
}


@article{alexov2021special,
  author = "E. Alexov",
  title = "Special Issue on Computational Chemistry Methods to Predict pKa’s of Ionizable Groups in Proteins, RNAs, DNAs and Small Molecules",
  year = 2021,
  journal = "Journal of Computational Biophysics and Chemistry",
  volume = 20,
  number = 2,
  pages = "109-110"
}


@article{li2021sampdi,
  author = "G. Li and S. Panday and Y. Peng and E. Alexov",
  title = "SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions.",
  year = 2021,
  journal = "Bioinformatics (Oxford, England)"
}


@article{wu2021opioid,
  author = "B. Wu and W. Hand and E. Alexov",
  title = "Opioid Addiction and Opioid Receptor Dimerization: Structural Modeling of the OPRD1 and OPRM1 Heterodimer and Its Signaling Pathways.",
  year = 2021,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",
  volume = 22,
  number = 19
}


@article{wang2021regularization,
  author = "S. Wang and E. Alexov and S. Zhao",
  title = "On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary [J]",
  year = 2021,
  journal = "Mathematical Biosciences and Engineering",
  volume = 18,
  number = 2,
  pages = "1370-1405"
}


@article{li2021saafec,
  author = "G. Li and S. K. Panday and E. Alexov",
  title = "SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability",
  year = 2021,
  journal = "International Journal of Molecular Sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 22,
  number = 2,
  pages = "606"
}


@article{shashikala2021bion,
  author = "H. Shashikala and A. Chakravorty and S. K. Panday and E. Alexov",
  title = "BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics",
  year = 2021,
  journal = "International Journal of Molecular Sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 22,
  number = 1,
  pages = "272"
}


@article{Wu2021b,
  author = "B. Wu and W. Hand and E. Alexov",
  title = "Opioid addiction and opioid receptor dimerization: structural modeling of the OPRD1 and OPRM1 heterodimer and its signaling pathways",
  year = 2021,
  journal = "International journal of molecular sciences",
  volume = 22,
  number = 19,
  pages = "10290"
}


@article{Li2021c,
  author = "G. Li and S. Panday and Y. Peng and E. Alexov",
  title = "SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions",
  year = 2021,
  journal = "Bioinformatics",
  volume = 37,
  number = 21,
  pages = "3760-3765"
}


@article{Alexov2021b,
  author = "E. Alexov",
  title = "Special Issue on Computational Chemistry Methods to Predict pKa’s of Ionizable Groups in Proteins, RNAs, DNAs and Small Molecules",
  year = 2021,
  journal = "Journal of Computational Biophysics and Chemistry",
  volume = 2,
  number = 2,
  pages = "109-110",
  doi = "10.1142/S2737416521020014",
  url = "https://www.worldscientific.com/doi/10.1142/S2737416521020014"
}


@article{alexov2021towards,
  author = "E. Alexov",
  title = "Towards More Biology-Oriented Papers: Name Change of the Journal of Theoretical and Computational Chemistry to Journal of Computational Biophysics and Chemistry",
  year = 2021,
  journal = "Journal of Computational Biophysics and Chemistry",
  publisher = "World Scientific Publishing Company",
  volume = 20,
  number = 1,
  pages = "1",
  doi = "10.1142/S2737416521010018"
}


@article{alexov2020ensemble,
  author = "E. Alexov and others",
  title = "An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants.",
  year = 2020,
  journal = "Genes",
  volume = 11,
  number = 9
}


@article{li2020newton,
  author = "C. Li and M. McGowan and E. Alexov and S. Zhao",
  title = "A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation [J]",
  year = 2020,
  journal = "Mathematical Biosciences and Engineering",
  volume = 17,
  number = 6,
  pages = "6259-6277"
}


@article{ranganathan2020ensemble,
  author = "S. R. Ganakammal and E. Alexov",
  title = "An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants",
  year = 2020,
  journal = "Genes",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 11,
  number = 9,
  pages = "1102"
}


@article{li2020saambe,
  author = "G. Li and S. Pahari and A. K. Murthy and S. Liang and R. Fragoza and H. Yu and E. Alexov",
  title = "SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein--protein binding affinity",
  year = 2020,
  journal = "Bioinformatics"
}


@article{koirala2020ab,
  author = "M. Koirala and E. Alexov",
  title = "Ab-initio binding of barnase--barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach",
  year = 2020,
  journal = "Journal of Theoretical and Computational Chemistry",
  publisher = "World Scientific Publishing Company",
  volume = 19,
  number = 4,
  pages = "2050016"
}


@article{lee2020mutations,
  author = "Y.-R. Lee and K. Khan and K. Armfield-Uhas and S. Srikanth and N. A. Thompson and M. Pardo and L. Yu and J. W. Norris and Y. Peng and K. W. Gripp and others",
  title = "Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy",
  year = 2020,
  journal = "Nature communications",
  publisher = "Nature Publishing Group",
  volume = 11,
  number = 1,
  pages = "1-17"
}


@article{peng2020ph,
  author = "Y. Peng and R. Kelle and C. Little and E. Michonova and K. G. Kornev and E. Alexov",
  title = "pH-dependent interactions of Apolipophorin-III with a lipid disk",
  year = 2020,
  journal = "Journal of Computational Biophysics and Chemistry",
  publisher = "World Scientific Publishing Company",
  pages = "1-12"
}


@article{ganakammal2020silico,
  author = "S. R. Ganakammal and M. Koirala and B. Wu and E. Alexov",
  title = "In-silico analysis to identify the role of MEN1 missense mutations in breast cancer",
  year = 2020,
  journal = "Journal of Theoretical and Computational Chemistry",
  publisher = "World Scientific Publishing Company",
  volume = 19,
  number = 6,
  pages = "2041002"
}


@article{pahari2020saambe,
  author = "S. Pahari and G. Li and A. K. Murthy and S. Liang and R. Fragoza and H. Yu and E. Alexov",
  title = "SAAMBE-3D: Predicting effect of mutations on protein--protein interactions",
  year = 2020,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 21,
  number = 7,
  pages = "2563"
}


@article{chakravorty2020capturing,
  author = "A. Chakravorty and S. Panday and S. Pahari and S. Zhao and E. Alexov",
  title = "Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi",
  year = 2020,
  journal = "Journal of chemical information and modeling",
  publisher = "American Chemical Society",
  volume = 60,
  number = 4,
  pages = "2229-2246"
}


@article{koirala2020computational,
  author = "M. Koirala and E. Alexov",
  title = "Computational Analysis of Missense Mutations in Creatine Transporter Protein Associated with Creatine Deficiency Syndrome",
  year = 2020,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 118,
  number = 3,
  pages = "197a"
}


@article{wang2020regularization,
  author = "S. Wang and A. Lee and E. Alexov and S. Zhao",
  title = "A regularization approach for solving Poisson’s equation with singular charge sources and diffuse interfaces",
  year = 2020,
  journal = "Applied Mathematics Letters",
  publisher = "Pergamon",
  volume = 102,
  pages = "106144"
}


@article{koirala2020computational,
  author = "M. Koirala and E. Alexov",
  title = "Computational chemistry methods to investigate the effects caused by DNA variants linked with disease",
  year = 2020,
  journal = "Journal of Theoretical and Computational Chemistry",
  publisher = "World Scientific Publishing Company",
  volume = 19,
  number = 6,
  pages = "1930001"
}


@inproceedings{pahari2019modeling,
  author = "S. Pahari and E. Alexov",
  title = "Modeling pKa without solute-water boundary: DelPhiPKa and its applications to protein-protein binding",
  year = 2019,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 258
}


@inproceedings{chakravorty2019effect,
  author = "A. Chakravorty and J. Higham and E. Alexov and R. Henchman",
  title = "Effect of water on the entropy of protein-protein binding",
  year = 2019,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 258
}


@article{panday2019reproducing,
  author = "S. K. Panday and M. H. Shashikala and A. Chakravorty and S. Zhao and E. Alexov",
  title = "Reproducing ensemble averaged electrostatics with Super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes",
  year = 2019,
  journal = "Communications in Information and Systems",
  volume = 19,
  number = 4
}


@article{ganakammal2019evaluation,
  author = "S. R. Ganakammal and E. Alexov",
  title = "Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: Application to Rett syndrome variants",
  year = 2019,
  journal = "PeerJ",
  publisher = "PeerJ Inc.",
  volume = 7,
  pages = "e8106"
}


@article{panday2019modeling,
  author = "S. K. Panday and M. H. Shashikala and M. Koirala and S. Pahari and A. Chakvorty and Y. Peng and L. Li and Z. Jia and C. Li and E. Alexov",
  title = "Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]",
  year = 2019,
  journal = "Living Journal of Computational Molecular Science",
  publisher = "University of Colorado Boulder",
  volume = 1,
  number = 2,
  pages = "10841"
}


@article{wu2019novel,
  author = "B. Wu and Y. Peng and J. Eggert and E. Alexov",
  title = "Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women",
  year = 2019,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 20,
  number = 19,
  pages = "4828"
}


@article{shashikala2019modeling,
  author = "H. Shashikala and A. Chakravorty and E. Alexov",
  title = "Modeling electrostatic force in protein-protein recognition",
  year = 2019,
  journal = "Frontiers in molecular biosciences",
  publisher = "Frontiers",
  volume = 6,
  pages = "94"
}


@article{peng2019dfmd,
  author = "Y. Peng and Y. Yang and L. Li and Z. Jia and W. Cao and E. Alexov",
  title = "DFMD: fast and effective DelPhiForce steered molecular dynamics approach to model ligand approach toward a receptor: Application to spermine synthase enzyme",
  year = 2019,
  journal = "Frontiers in molecular biosciences",
  publisher = "Frontiers",
  volume = 6,
  pages = "74"
}


@article{li2019delphi,
  author = "C. Li and Z. Jia and A. Chakravorty and S. Pahari and Y. Peng and S. Basu and M. Koirala and S. K. Panday and M. Petukh and L. Li and others",
  title = "DelPhi suite: New developments and review of functionalities",
  year = 2019,
  journal = "Journal of computational chemistry",
  publisher = "John Wiley \& Sons, Inc. Hoboken, USA",
  volume = 40,
  number = 28,
  pages = "2502-2508"
}


@article{tajielyato2019modeling,
  author = "N. Tajielyato and E. Alexov",
  title = "Modeling pKas of unfolded proteins to probe structural models of unfolded state",
  year = 2019,
  journal = "Journal of Theoretical and Computational Chemistry",
  publisher = "World Scientific Publishing Company",
  volume = 18,
  number = 4,
  pages = "1950020"
}


@article{hazra2019super,
  author = "T. Hazra and S. A. Ullah and S. Wang and E. Alexov and S. Zhao",
  title = "A super-Gaussian Poisson--Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states",
  year = 2019,
  journal = "Journal of mathematical biology",
  publisher = "Springer Berlin Heidelberg",
  volume = 79,
  number = 2,
  pages = "631-672"
}


@article{spellicy2019three,
  author = "C. J. Spellicy and Y. Peng and L. Olewiler and S. S. Cathey and R. C. Rogers and D. Bartholomew and J. Johnson and E. Alexov and J. A. Lee and M. J. Friez and others",
  title = "Three additional patients with EED-associated overgrowth: potential mutation hotspots identified?",
  year = 2019,
  journal = "Journal of human genetics",
  publisher = "Nature Publishing Group",
  volume = 64,
  number = 6,
  pages = "561-572"
}


@article{tajielyato2019processivity,
  author = "N. Tajielyato and E. Alexov",
  title = "Processivity vs. beating: Comparing cytoplasmic and axonemal dynein microtubule binding domain association with microtubule",
  year = 2019,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 20,
  number = 5,
  pages = "1090"
}


@article{pahari2019pkad,
  author = "S. Pahari and L. Sun and E. Alexov",
  title = "PKAD: a database of experimentally measured pKa values of ionizable groups in proteins",
  year = 2019,
  journal = "Database",
  publisher = "Oxford Academic",
  volume = 2019
}


@article{bosthanthirige2019modeling,
  author = "M. S. H. Bosthanthirige and A. Chakravorty and E. Alexov",
  title = "Modeling Electrostatic Force in Protein-Protein Recognition",
  year = 2019,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 116,
  number = 3,
  pages = "46a"
}


@article{chakravorty2019new,
  author = "A. Chakravorty and J. Higham and E. Alexov and R. H. Henchman",
  title = "New method to determine the effect of dimerization on protein flexibility from molecular dynamics simulation using structural hierarchy",
  year = 2019,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 116,
  number = 3,
  pages = "561a-562a"
}


@article{tajielyato2019comparative,
  author = "N. Tajielyato and J. Alper and E. Alexov",
  title = "Comparative Study of Flagellar and Cytoplasmic Dyneins",
  year = 2019,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 116,
  number = 3,
  pages = "560a"
}


@article{pahari2019surface,
  author = "S. Pahari and L. Sun and E. Alexov",
  title = "Surface-Free Protocol for Computing PKA's (DelPhiPKa): Applications to Protein-Protein Interactions",
  year = 2019,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 116,
  number = 3,
  pages = "166a"
}


@article{wu2019investigating,
  author = "B. Wu and Y. Peng and J. A. Eggert and E. Alexov",
  title = "Investigating the Effects of Missense Mutations in MSH2 Gene Associated with Lynch Syndrome",
  year = 2019,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 116,
  number = 3,
  pages = "192a"
}


@article{peng2019electrostatic,
  author = "Y. Peng and M. Koirala and E. Alexov",
  title = "Electrostatic Force Driven Molecular Dynamics Simulations",
  year = 2019,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 116,
  number = 3,
  pages = "290a"
}


@article{chakravorty2019grid,
  author = "A. Chakravorty and E. Gallicchio and E. Alexov",
  title = "A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry",
  year = 2019,
  journal = "Journal of computational chemistry",
  publisher = "John Wiley \& Sons, Inc. Hoboken, USA",
  volume = 40,
  number = 12,
  pages = "1290-1304"
}


@article{peng2019structural,
  author = "Y. Peng and E. Alexov and S. Basu",
  title = "Structural perspective on revealing and altering molecular functions of genetic variants linked with diseases",
  year = 2019,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 20,
  number = 3,
  pages = "548"
}


@article{peng2018structural,
  author = "Y. Peng and E. Alexov and S. Basu",
  title = "Structural Perspective on Revealing and Altering Molecular Mechanisms of Genetic Variants Linked with Diseases",
  year = 2018
}


@inproceedings{tajielyato2018modeling,
  author = "N. Tajielyato and J. Alper and E. Alexov",
  title = "Modeling Tubulin E-Hooks Interactions with Dynein Microtubule Binding Domain",
  year = 2018,
  booktitle = "PROTEIN SCIENCE",
  volume = 27,
  pages = "198-198"
}


@article{pahari2018delphipka,
  author = "S. Pahari and L. Sun and S. Basu and E. Alexov",
  title = "DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate",
  year = 2018,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  publisher = "John Wiley \& Sons, Inc. Hoboken, USA",
  volume = 86,
  number = 12,
  pages = "1277-1283"
}


@article{tajielyato2018hooks,
  author = "N. Tajielyato and L. Li and Y. Peng and J. Alper and E. Alexov",
  title = "E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein",
  year = 2018,
  journal = "Scientific reports",
  publisher = "Nature Publishing Group",
  volume = 8,
  number = 1,
  pages = "1-10"
}


@article{chakravorty2018gaussian,
  author = "A. Chakravorty and Z. Jia and Y. Peng and N. Tajielyato and L. Wang and E. Alexov",
  title = "Gaussian-based smooth dielectric function: a surface-free approach for modeling macromolecular binding in solvents",
  year = 2018,
  journal = "Frontiers in molecular biosciences",
  publisher = "Frontiers",
  volume = 5,
  pages = "25"
}


@article{jia2018capricious,
  author = "Z. Jia and L. Li and Y. Peng and F. Ding and E. Alexov",
  title = "The capricious electrostatic force: Revealing the signaling pathway in integrin $\alpha$ 2-I domain",
  year = 2018,
  journal = "Journal of Theoretical and Computational Chemistry",
  publisher = "World Scientific Publishing Company",
  volume = 17,
  number = 3,
  pages = "1840001"
}


@article{godar2018single,
  author = "S. C. Godar and H. Lovelace and J. Eller and M. Spencer and L. Li and G. Hamilton and H. Sanabria and E. Alexov and J. Alper",
  title = "Single Molecule Study of Long-Range Electrostatic Binding Affinity of Cytoplasmic Dynein's Microtubule Binding Domain",
  year = 2018,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 114,
  number = 3,
  pages = "512a"
}


@article{spellicy2018key,
  author = "C. J. Spellicy and J. Norris and R. Bend and C. Bupp and P. Mester and T. Reynolds and J. Dean and Y. Peng and E. Alexov and C. E. Schwartz and others",
  title = "Key apoptotic genes APAF1 and CASP9 implicated in recurrent folate-resistant neural tube defects",
  year = 2018,
  journal = "European Journal of Human Genetics",
  publisher = "Nature Publishing Group",
  volume = 26,
  number = 3,
  pages = "420-427"
}


@article{chakravorty2018reproducing,
  author = "A. Chakravorty and Z. Jia and L. Li and S. Zhao and E. Alexov",
  title = "Reproducing the ensemble average polar solvation energy of a protein from a single structure: gaussian-based smooth dielectric function for macromolecular modeling",
  year = 2018,
  journal = "Journal of chemical theory and computation",
  publisher = "American Chemical Society",
  volume = 14,
  number = 2,
  pages = "1020-1032"
}


@article{peng2018computational,
  author = "Y. Peng and R. Myers and W. Zhang and E. Alexov",
  title = "Computational investigation of the missense mutations in DHCR7 gene associated with Smith-Lemli-Opitz syndrome",
  year = 2018,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 19,
  number = 1,
  pages = "141"
}


@article{peng2018predicting,
  author = "Y. Peng and L. Sun and Z. Jia and L. Li and E. Alexov",
  title = "Predicting protein--DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver",
  year = 2018,
  journal = "Bioinformatics",
  publisher = "Oxford University Press",
  volume = 34,
  number = 5,
  pages = "779-786"
}


@article{vaidyanathan2017identification,
  author = "K. Vaidyanathan and T. Niranjan and N. Selvan and C. F. Teo and M. May and S. Patel and B. Weatherly and C. Skinner and J. Opitz and J. Carey and others",
  title = "Identification and characterization of a missense mutation in the O-linked $\beta$-N-acetylglucosamine (O-GlcNAc) transferase gene that segregates with X-linked intellectual disability",
  year = 2017,
  journal = "Journal of Biological Chemistry",
  publisher = "Elsevier",
  volume = 292,
  number = 21,
  pages = "8948-8963"
}


@inproceedings{jia2017simulation,
  author = "Z. Jia and E. Alexov",
  title = "Simulation study of integrin alpha-2 I domain activation",
  year = 2017,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 254
}


@inproceedings{peng2017predicting,
  author = "Y. Peng and E. Alexov",
  title = "Predicting binding free energy change caused by missense mutations in protein-DNA interactions using modified MM/PBSA method",
  year = 2017,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 254
}


@inproceedings{selvan2017identification,
  author = "N. Selvan and K. Vaidyanathan and S. George and T. Niranjan and C. F. Teo and M. May and S. Patel and B. Weatherly and J. Opitz and J. Carey and others",
  title = "Identification and Characterization of Multiple Missense Mutations in the O-GlcNAc transferase gene that are causal for X-linked Intellectual Disability",
  year = 2017,
  booktitle = "GLYCOBIOLOGY",
  volume = 27,
  number = 12,
  pages = "1187-1187"
}


@article{li2017forces,
  author = "L. Li and Z. Jia and Y. Peng and S. Godar and I. Getov and S. Teng and J. Alper and E. Alexov",
  title = "Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations",
  year = 2017,
  journal = "Scientific reports",
  publisher = "Nature Publishing Group",
  volume = 7,
  number = 1,
  pages = "1-12"
}


@article{pengprotein,
  author = "Y. Peng and E. Alexov",
  title = "Protein Conformational Disease: Visit the Facts at a Glance",
  year = 2017,
  journal = "eLS",
  publisher = "American Cancer Society",
  pages = "1-7"
}


@article{li2017delphiforce,
  author = "L. Li and Z. Jia and Y. Peng and A. Chakravorty and L. Sun and E. Alexov",
  title = "DelPhiForce web server: electrostatic forces and energy calculations and visualization",
  year = 2017,
  journal = "Bioinformatics",
  publisher = "Oxford University Press",
  volume = 33,
  number = 22,
  pages = "3661-3663"
}


@article{hoffman2017cytoskeletal,
  author = "L. Hoffman and L. Li and E. Alexov and H. Sanabria and M. N. Waxham",
  title = "Cytoskeletal-like Filaments of Ca2+-Calmodulin-Dependent Protein Kinase II Are Formed in a Regulated and Zn2+-Dependent Manner",
  year = 2017,
  journal = "Biochemistry",
  publisher = "American Chemical Society",
  volume = 56,
  number = 15,
  pages = "2149-2160"
}


@article{vaidyanathan2017identification,
  author = "K. Vaidyanathan and T. Niranjan and N. Selvan and C. F. Teo and M. May and S. Patel and B. Weatherly and C. Skinner and J. Opitz and J. Carey and others",
  title = "Identification and characterization of a missense mutation in the O-GlcNAc transferase gene that segregates with X-linked intellectual disability",
  year = 2017,
  journal = "J. Biol. Chem",
  volume = 292,
  pages = "8948-8963"
}


@article{chakravorty2017new,
  author = "A. Chakravorty and Z. Jia and L. Li and E. Alexov",
  title = "A new DelPhi feature for modeling electrostatic potential around proteins: Role of bound ions and implications for zeta-potential",
  year = 2017,
  journal = "Langmuir",
  publisher = "American Chemical Society",
  volume = 33,
  number = 9,
  pages = "2283-2295"
}


@article{hoffman2017calcium,
  author = "L. Hoffman and L. Li and E. Alexov and M. N. Waxham and H. Sanabria",
  title = "Calcium Calmodulin Regulates Zinc Mediated Changes in the Structure, Self-Association, and Activity of CaMKII",
  year = 2017,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 112,
  number = 3,
  pages = "444a-445a"
}


@article{li2017multi,
  author = "L. Li and J. Alper and E. Alexov",
  title = "Multi-Scale Investigation on the Mechanisms of Dyneins’ Motion on Microtubule",
  year = 2017,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 112,
  number = 3,
  pages = "261a"
}


@article{li2017delphiforce,
  author = "L. Li and A. Chakravorty and E. Alexov",
  title = "DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding",
  year = 2017,
  journal = "Journal of computational chemistry",
  volume = 38,
  number = 9,
  pages = "584-593"
}


@article{peng2017computational,
  author = "Y. Peng and E. Alexov",
  title = "Computational investigation of proton transfer, p K a shifts and p H-optimum of protein--DNA and protein--RNA complexes",
  year = 2017,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  volume = 85,
  number = 2,
  pages = "282-295"
}


@inproceedings{alexov2016parallelization,
  author = "E. Alexov",
  title = "Parallelization schemes for solving Poisson-Boltzmann equation via finite-difference method: Implementations in DelPhi and applications",
  year = 2016,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 252
}


@article{campbell2016dielectric,
  author = "B. Campbell and L. Li and E. Alexov",
  title = "Dielectric Properties of Biological Macromolecules and Biomolecule--Water Interfaces",
  year = 2016,
  journal = "Encyclopedia of Biocolloid and Biointerface Science 2V Set",
  publisher = "John Wiley \& Sons, Inc. Hoboken, NJ, USA",
  pages = "380-390"
}


@article{peng2016cofactors,
  author = "Y. Peng and E. Alexov",
  title = "Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model",
  year = 2016,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  volume = 84,
  number = 12,
  pages = "1797-1809"
}


@article{chakavorty2016electrostatic,
  author = "A. Chakavorty and L. Li and E. Alexov",
  title = "Electrostatic component of binding energy: interpreting predictions from poisson--boltzmann equation and modeling protocols",
  year = 2016,
  journal = "Journal of computational chemistry",
  volume = 37,
  number = 28,
  pages = "2495-2507"
}


@article{li2016cytoplasmic,
  author = "L. Li and J. Alper and E. Alexov",
  title = "Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions",
  year = 2016,
  journal = "Scientific reports",
  publisher = "Nature Publishing Group",
  volume = 6,
  number = 1,
  pages = "1-12"
}


@article{yang2016binding,
  author = "Y. Yang and T. G. Kucukkal and J. Li and E. Alexov and W. Cao",
  title = "Binding analysis of methyl-CpG binding domain of MeCP2 and Rett syndrome mutations",
  year = 2016,
  journal = "ACS chemical biology",
  publisher = "American Chemical Society",
  volume = 11,
  number = 10,
  pages = "2706-2715"
}


@article{petukh2016saambe,
  author = "M. Petukh and L. Dai and E. Alexov",
  title = "SAAMBE: webserver to predict the charge of binding free energy caused by amino acids mutations",
  year = 2016,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 17,
  number = 4,
  pages = "547"
}


@article{peng2016revealing,
  author = "Y. Peng and J. Norris and C. Schwartz and E. Alexov",
  title = "Revealing the effects of missense mutations causing Snyder-Robinson syndrome on the stability and dimerization of spermine synthase",
  year = 2016,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 17,
  number = 1,
  pages = "77"
}


@article{getov2016saafec,
  author = "I. Getov and M. Petukh and E. Alexov",
  title = "SAAFEC: predicting the effect of single point mutations on protein folding free energy using a knowledge-modified MM/PBSA approach",
  year = 2016,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 17,
  number = 4,
  pages = "512"
}


@article{li2016multiscale,
  author = "L. Li and J. Alper and E. Alexov",
  title = "Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules",
  year = 2016,
  journal = "Scientific reports",
  publisher = "Nature Publishing Group",
  volume = 6,
  number = 1,
  pages = "1-12"
}


@article{wang2016delphipka,
  author = "L. Wang and M. Zhang and E. Alexov",
  title = "DelPhiPKa web server: predicting p K a of proteins, RNAs and DNAs",
  year = 2016,
  journal = "Bioinformatics",
  publisher = "Oxford University Press",
  volume = 32,
  number = 4,
  pages = "614-615"
}


@article{peng2016investigating,
  author = "Y. Peng and E. Alexov",
  title = "Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding",
  year = 2016,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  volume = 84,
  number = 2,
  pages = "232-239"
}


@inproceedings{getov2015predicting,
  author = "I. Getov and M. Petukh and E. Alexov",
  title = "Predicting folding free energy changes caused by single point mutations via combined usage of MM-PBSA method and biophysical characteristics",
  year = 2015,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 250
}


@article{tavtigian2015shotgun,
  author = "S. V. Tavtigian",
  title = "Shotgun Approach to Functional Annotation of Genes",
  year = 2015,
  journal = "Human Mutation",
  volume = 36,
  number = 2,
  pages = "v-v"
}


@article{alexov2015navigating,
  author = "E. Alexov",
  title = "Navigating through genomics data to deliver testable predictions",
  year = 2015,
  journal = "Human Mutation",
  volume = 36,
  number = 2,
  pages = "v-v"
}


@article{petukh2015sambe,
  author = "M. Petukh and J. Morrison and M. Li and A. Panchenko and E. Alexov",
  title = "SAMBE: The New Webserver for Predicting the Effect of nssNP on the Protein-Protein Binding Free Energy",
  year = 2015,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 108,
  number = 2,
  pages = "157a-158a"
}


@article{petukh2015statistical,
  author = "M. Petukh and M. Zhang and E. Alexov",
  title = "Statistical investigation of surface bound ions and further development of BION server to include p H and salt dependence",
  year = 2015,
  journal = "Journal of computational chemistry",
  volume = 36,
  number = 32,
  pages = "2381-2393"
}


@article{may2015zc4h2,
  author = "M. May and K.-S. Hwang and J. Miles and C. Williams and T. Niranjan and S. G. Kahler and P. Chiurazzi and K. Steindl and P. J. V. D. Spek and S. Swagemakers and others",
  title = "ZC4H2, an XLID gene, is required for the generation of a specific subset of CNS interneurons",
  year = 2015,
  journal = "Human molecular genetics",
  publisher = "Oxford University Press",
  volume = 24,
  number = 17,
  pages = "4848-4861"
}


@article{kucukkal2015structural,
  author = "T. G. Kucukkal and E. Alexov",
  title = "Structural, dynamical, and energetical consequences of Rett syndrome mutation R133C in MeCP2",
  year = 2015,
  journal = "Computational and mathematical methods in medicine",
  publisher = "Hindawi",
  volume = 2015
}


@article{kucukkal2015impact,
  author = "T. G. Kucukkal and Y. Yang and O. Uvarov and W. Cao and E. Alexov",
  title = "Impact of rett syndrome mutations on MeCP2 MBD stability",
  year = 2015,
  journal = "Biochemistry",
  publisher = "American Chemical Society",
  volume = 54,
  number = 41,
  pages = "6357-6368"
}


@article{peng2015mutations,
  author = "Y. Peng and J. Suryadi and Y. Yang and T. G. Kucukkal and W. Cao and E. Alexov",
  title = "Mutations in the KDM5C ARID domain and their plausible association with syndromic Claes-Jensen-Type disease",
  year = 2015,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 16,
  number = 11,
  pages = "27270-27287"
}


@article{li2015energy,
  author = "L. Li and L. Wang and E. Alexov",
  title = "On the energy components governing molecular recognition in the framework of continuum approaches",
  year = 2015,
  journal = "Frontiers in molecular biosciences",
  publisher = "Frontiers",
  volume = 2,
  pages = "5"
}


@article{petukh2015predicting,
  author = "M. Petukh and M. Li and E. Alexov",
  title = "Predicting binding free energy change caused by point mutations with knowledge-modified MM/PBSA method",
  year = 2015,
  journal = "PLoS computational biology",
  publisher = "Public Library of Science San Francisco, CA USA",
  volume = 11,
  number = 7,
  pages = "e1004276"
}


@article{wang2015pka,
  author = "L. Wang and L. Li and E. Alexov",
  title = "pKa predictions for proteins, RNA s, and DNA s with the Gaussian dielectric function using DelPhi pKa",
  year = 2015,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  volume = 83,
  number = 12,
  pages = "2186-2197"
}


@article{petukh2015human,
  author = "M. Petukh and T. G. Kucukkal and E. Alexov",
  title = "On human disease-causing amino acid variants: Statistical study of sequence and structural patterns",
  year = 2015,
  journal = "Human mutation",
  volume = 36,
  number = 5,
  pages = "524-534"
}


@article{kucukkal2015structural,
  author = "T. G. Kucukkal and M. Petukh and L. Li and E. Alexov",
  title = "Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins",
  year = 2015,
  journal = "Current opinion in structural biology",
  publisher = "Elsevier Current Trends",
  volume = 32,
  pages = "18-24"
}


@article{zhang2014rational,
  author = "Z. Zhang and V. Martiny and D. Lagorce and Y. Ikeguchi and E. Alexov and others",
  title = "Rational Design of Small-Molecule Stabilizers of Spermine Synthase Dimer by Virtual",
  year = 2014
}


@inproceedings{li2014modeling,
  author = "L. Li and N. Smith and E. Alexov",
  title = "Modeling ensemble-averaged electrostatics with smooth Gaussian-based dielectric function",
  year = 2014,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 248
}


@article{wu2014molecular,
  author = "B. Wu and J. Eggert and E. Alexov",
  title = "Molecular mechanisms underlying pathogenic missense mutations",
  year = 2014,
  journal = "eLS",
  publisher = "American Cancer Society"
}


@article{campbell2014electrostatic,
  author = "B. Campbell and M. Petukh and E. Alexov and C. Li",
  title = "On the electrostatic properties of homodimeric proteins",
  year = 2014,
  journal = "Journal of Theoretical and Computational Chemistry",
  publisher = "World Scientific Publishing Company",
  volume = 13,
  number = 3,
  pages = "1440007"
}


@article{petukh2014ion,
  author = "M. Petukh and E. Alexov",
  title = "Ion binding to biological macromolecules",
  year = 2014,
  journal = "Asian journal of physics: an international quarterly research journal",
  publisher = "NIH Public Access",
  volume = 23,
  number = 5,
  pages = "735"
}


@article{nedumpully2014structural,
  author = "P. Nedumpully-Govindan and L. Li and E. G. Alexov and M. A. Blenner and F. Ding",
  title = "Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity",
  year = 2014,
  journal = "Bioinformatics",
  publisher = "Oxford University Press",
  volume = 30,
  number = 16,
  pages = "2302-2309"
}


@article{alexov2014advances,
  author = "E. Alexov",
  title = "Advances in human biology: combining genetics and molecular biophysics to pave the way for personalized diagnostics and medicine",
  year = 2014,
  journal = "Advances in Biology",
  publisher = "Hindawi",
  volume = 2014
}


@article{petukh2014chronic,
  author = "M. Petukh and B. Wu and S. Stefl and N. Smith and D. Hyde-Volpe and L. Wang and E. Alexov",
  title = "Chronic beryllium disease: revealing the role of beryllium ion and small peptides binding to HLA-DP2",
  year = 2014,
  journal = "PLoS One",
  publisher = "Public Library of Science",
  volume = 9,
  number = 11,
  pages = "e111604"
}


@article{kimmett2014problm,
  author = "T. Kimmett and N. Smith and S. Witham and M. Petukh and S. Sarkar and E. Alexov",
  title = "ProBLM web server: protein and membrane placement and orientation package",
  year = 2014,
  journal = "Computational and mathematical methods in medicine",
  publisher = "Hindawi",
  volume = 2014
}


@article{dias2014modeling,
  author = "R. P. Dias and L. Li and T. A. Soares and E. Alexov",
  title = "Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: the MEMPOT algorithm implemented in DelPhi",
  year = 2014,
  journal = "Journal of computational chemistry",
  volume = 35,
  number = 19,
  pages = "1418-1429"
}


@article{li2014modeling,
  author = "L. Li and C. Li and E. Alexov",
  title = "On the modeling of polar component of solvation energy using smooth Gaussian-based dielectric function",
  year = 2014,
  journal = "Journal of Theoretical and Computational Chemistry",
  publisher = "World Scientific Publishing Company",
  volume = 13,
  number = 3,
  pages = "1440002"
}


@article{zhang2014rational,
  author = "Z. Zhang and V. Martiny and D. Lagorce and Y. Ikeguchi and E. Alexov and M. A. Miteva",
  title = "Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach",
  year = 2014,
  journal = "PLoS One",
  publisher = "Public Library of Science",
  volume = 9,
  number = 10,
  pages = "e110884"
}


@article{dolzhanskaya2014novel,
  author = "N. Dolzhanskaya and M. A. Gonzalez and F. Sperziani and S. Stefl and J. Messing and G. Y. Wen and E. Alexov and S. Zuchner and M. Velinov",
  title = "A novel p. Leu (381) Phe mutation in presenilin 1 is associated with very early onset and unusually fast progressing dementia as well as lysosomal inclusions typically seen in Kufs disease",
  year = 2014,
  journal = "Journal of Alzheimer's Disease",
  publisher = "IOS Press",
  volume = 39,
  number = 1,
  pages = "23-27"
}


@article{kucukkal2014computational,
  author = "T. G. Kucukkal and Y. Yang and S. C. Chapman and W. Cao and E. Alexov",
  title = "Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics",
  year = 2014,
  journal = "International journal of molecular sciences",
  publisher = "Multidisciplinary Digital Publishing Institute",
  volume = 15,
  number = 6,
  pages = "9670-9717"
}


@article{li2014predicting,
  author = "M. Li and M. Petukh and E. Alexov and A. R. Panchenko",
  title = "Predicting the impact of missense mutations on protein--protein binding affinity",
  year = 2014,
  journal = "Journal of chemical theory and computation",
  publisher = "American Chemical Society",
  volume = 10,
  number = 4,
  pages = "1770-1780"
}


@article{boccuto2014mutation,
  author = "L. Boccuto and K. Aoki and H. Flanagan-Steet and C.-F. Chen and X. Fan and F. Bartel and M. Petukh and A. Pittman and R. Saul and A. Chaubey and others",
  title = "A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt \& pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation",
  year = 2014,
  journal = "Human molecular genetics",
  publisher = "Oxford University Press",
  volume = 23,
  number = 2,
  pages = "418-433"
}


@article{das2013simple,
  author = "A. Das and M. Gur and I. Bahar and B. Roux",
  title = "A simple coarse-grained model to map the transition pathway between two stable conformations using the anisotropic elastic network model",
  year = 2013,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 104,
  number = 2,
  pages = "35a-36a"
}


@inproceedings{alexov2013electrostatics,
  author = "E. Alexov",
  title = "Electrostatics and polarization effects in biophysical chemistry: In silico, in vitro, and in vivo",
  year = 2013,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 246
}


@inproceedings{petukh2013electrostatics,
  author = "M. Petukh and A. Panchenko and E. Alexov",
  title = "Electrostatics plays significant role in changes of the protein-protein affinity due to missense mutations",
  year = 2013,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 246
}


@inproceedings{li2013smooth,
  author = "L. Li and C. Li and E. Alexov",
  title = "Smooth dielectric function for modeling electrostatics in biological macromolecules",
  year = 2013,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 246
}


@article{li2013multi,
  author = "C. Li and M. Petukh and L. Li and E. Alexov",
  title = "Multi-Level and Interleaved Poisson-Boltzmann (MLIPB) Method for Parallel Computing of the Electrostatics and its Application in Delphi",
  year = 2013,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 104,
  number = 2,
  pages = "507a"
}


@inproceedings{vaidyanathan2013characterizing,
  author = "K. Vaidyanathan and T. Niranjan and M. May and R. Rose and C. F. Teo and S. Prabakaran and R. Bridger and E. Alexov and T. Wang and C. Schwartz and others",
  title = "Characterizing a missense mutation in O-GlcNAc transferase that segregates with disease in a family with X-linked Intellectual Disability",
  year = 2013,
  booktitle = "GLYCOBIOLOGY",
  volume = 23,
  number = 11,
  pages = "1334-1335"
}


@inproceedings{zhang2013snyder,
  author = "Z. Zhang and V. Martiny and D. Lagorce and E. Alexov and M. Miteva and others",
  title = "Snyder-Robinson Syndrome: Rescuing the Disease-Causing Effect of G56S mutant by Small Molecule Binding",
  year = 2013,
  booktitle = "APS March Meeting Abstracts",
  volume = 2013,
  pages = "G45-005"
}


@article{li2013modeling,
  author = "L. Li and C. Li and E. Alexov",
  title = "Modeling Proteins and Small Molecules with Inhomogeneous Dielectric Function: Implementation in Delphi",
  year = 2013,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 104,
  number = 2,
  pages = "35a"
}


@article{alexov2013preface,
  author = "E. Alexov and G.-W. Wei",
  title = "Preface: Special Issue on Modeling Electrostatics in Molecular Biology (MEMB)",
  year = 2013,
  journal = "Communications in Computational Physics",
  publisher = "Cambridge University Press",
  volume = 13,
  number = 1,
  pages = "i-v"
}


@article{zhang2013enhancing,
  author = "Z. Zhang and A. Pegg and Y. Ikeguchi and E. Alexov",
  title = "Enhancing Human Spermine Synthase Activity by Site Directed Mutations",
  year = 2013,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 104,
  number = 2,
  pages = "380a"
}


@article{petukh2013predicting,
  author = "M. Petukh and C. Li and E. Alexov",
  title = "Predicting non-specifically bound ions: Application to BION webserver and beryllium disease",
  year = 2013,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 104,
  number = 2,
  pages = "506a"
}


@article{petukh2013bion,
  author = "M. Petukh and T. Kimmet and E. Alexov",
  title = "BION web server: predicting non-specifically bound surface ions",
  year = 2013,
  journal = "Bioinformatics",
  publisher = "Oxford University Press",
  volume = 29,
  number = 6,
  pages = "805-806"
}


@article{alexov2013understanding,
  author = "E. Alexov and M. Sternberg",
  title = "Understanding molecular effects of naturally occurring genetic differences.",
  year = 2013,
  journal = "Journal of molecular biology",
  volume = 425,
  number = 21,
  pages = "3911-3913"
}


@article{li2013continuous,
  author = "C. Li and M. Petukh and L. Li and E. Alexov",
  title = "Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi",
  year = 2013,
  journal = "Journal of computational chemistry",
  publisher = "Wiley Online Library",
  volume = 34,
  number = 22,
  pages = "1949-1960"
}


@article{wang2013silico,
  author = "L. Wang and S. Witham and Z. Zhang and L. Li and M. E. Hodsdon and E. Alexov",
  title = "In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor",
  year = 2013,
  journal = "Communications in computational physics",
  publisher = "NIH Public Access",
  volume = 13,
  number = 1,
  pages = "207"
}


@article{zhang2013rational,
  author = "Z. Zhang and S. Witham and M. Petukh and G. Moroy and M. Miteva and Y. Ikeguchi and E. Alexov",
  title = "A rational free energy-based approach to understanding and targeting disease-causing missense mutations",
  year = 2013,
  journal = "Journal of the American Medical Informatics Association",
  publisher = "BMJ Publishing Group BMA House, Tavistock Square, London, WC1H 9JR",
  volume = 20,
  number = 4,
  pages = "643-651"
}


@article{zhang2013enhancing,
  author = "Z. Zhang and Y. Zheng and M. Petukh and A. Pegg and Y. Ikeguchi and E. Alexov",
  title = "Enhancing human spermine synthase activity by engineered mutations",
  year = 2013,
  journal = "PLoS Comput Biol",
  publisher = "Public Library of Science",
  volume = 9,
  number = 2,
  pages = "e1002924"
}


@article{sarkar2013delphi,
  author = "S. Sarkar and S. Witham and J. Zhang and M. Zhenirovskyy and W. Rocchia and E. Alexov",
  title = "DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes",
  year = 2013,
  journal = "Communications in computational physics",
  publisher = "NIH Public Access",
  volume = 13,
  number = 1,
  pages = "269"
}


@article{wang2013using,
  author = "L. Wang and Z. Zhang and W. Rocchia and E. Alexov",
  title = "Using DelPhi capabilities to mimic protein’s conformational reorganization with amino acid specific dielectric constants",
  year = 2013,
  journal = "Communications in computational physics",
  publisher = "NIH Public Access",
  volume = 13,
  number = 1,
  pages = "13"
}


@article{li2013progress,
  author = "C. Li and L. Li and M. Petukh and E. Alexov",
  title = "Progress in developing Poisson-Boltzmann equation solvers",
  year = 2013,
  journal = "Computational and Mathematical Biophysics",
  publisher = "De Gruyter",
  volume = 1,
  number = 1,
  pages = "42-62"
}


@article{zhang2013y328c,
  author = "Z. Zhang and J. Norris and V. Kalscheuer and T. Wood and L. Wang and C. Schwartz and E. Alexov and H. V. Esch",
  title = "A Y328C missense mutation in spermine synthase causes a mild form of Snyder--Robinson syndrome",
  year = 2013,
  journal = "Human molecular genetics",
  publisher = "Oxford University Press",
  volume = 22,
  number = 18,
  pages = "3789-3797"
}


@article{petukh2013role,
  author = "M. Petukh and S. Stefl and E. Alexov",
  title = "The role of protonation states in ligand-receptor recognition and binding",
  year = 2013,
  journal = "Current pharmaceutical design",
  publisher = "Bentham Science Publishers",
  volume = 19,
  number = 23,
  pages = "4182-4190"
}


@article{decherchi2013between,
  author = "S. Decherchi and J. Colmenares and C. E. Catalano and M. Spagnuolo and E. Alexov and W. Rocchia",
  title = "Between algorithm and model: different molecular surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution",
  year = 2013,
  journal = "Communications in computational physics",
  publisher = "NIH Public Access",
  volume = 13,
  pages = "61"
}


@article{onufriev2013protonation,
  author = "A. V. Onufriev and E. Alexov",
  title = "Protonation and pK changes in protein-ligand binding",
  year = 2013,
  journal = "Quarterly reviews of biophysics",
  publisher = "NIH Public Access",
  volume = 46,
  number = 2,
  pages = "181"
}


@article{nishi2013cancer,
  author = "H. Nishi and M. Tyagi and S. Teng and B. A. Shoemaker and K. Hashimoto and E. Alexov and S. Wuchty and A. R. Panchenko",
  title = "Cancer missense mutations alter binding properties of proteins and their interaction networks",
  year = 2013,
  journal = "PloS one",
  publisher = "Public Library of Science",
  volume = 8,
  number = 6,
  pages = "e66273"
}


@article{stefl2013molecular,
  author = "S. Stefl and H. Nishi and M. Petukh and A. R. Panchenko and E. Alexov",
  title = "Molecular mechanisms of disease-causing missense mutations",
  year = 2013,
  journal = "Journal of molecular biology",
  publisher = "Academic Press",
  volume = 425,
  number = 21,
  pages = "3919-3936"
}


@article{li2013dielectric,
  author = "L. Li and C. Li and Z. Zhang and E. Alexov",
  title = "On the dielectric “constant” of proteins: smooth dielectric function for macromolecular modeling and its implementation in DelPhi",
  year = 2013,
  journal = "Journal of chemical theory and computation",
  publisher = "American Chemical Society",
  volume = 9,
  number = 4,
  pages = "2126-2136"
}


@inproceedings{li2012parallelized,
  author = "C. Li and L. Li and E. Alexov",
  title = "Parallelized DelPhi: A multiprocessor Poisson-Boltzmann solver to calculate electrostatic energies of biological macromolecules",
  year = 2012,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 244
}


@article{gunner2012calculation,
  author = "M. R. GUNNER and E. ALEXOV",
  title = "CALCULATION OF ELECTROSTATIC FORCES",
  year = 2012,
  journal = "Molecular Modeling and Dynamics of Bioinorganic Systems",
  publisher = "Springer Science \& Business Media",
  volume = 41,
  pages = "361"
}


@article{li2012new,
  author = "C. Li and M. Zhenirovskyy and L. Li and E. Alexov",
  title = "New Parallelized DelPhi: Fast and Efficient Poisson-Boltzmann Solver to Calculate Electrostatics of Large Supramolecular Structures",
  year = 2012,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 102,
  number = 3,
  pages = "270a"
}


@article{witham2012modeling,
  author = "S. Witham and E. Alexov",
  title = "Modeling CLIC2-RyR Interactions and the Effect of Disease Causing Mutation",
  year = 2012,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 102,
  number = 3,
  pages = "456a"
}


@inproceedings{li2012effect,
  author = "L. Li and L. Wang and C. Li and E. Alexov",
  title = "Effect of non-uniform protein dielectric constant on the electrostatic energy calculations",
  year = 2012,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 244
}


@article{smith2012protein,
  author = "N. Smith and B. Campbell and L. Li and C. Li and E. Alexov",
  title = "Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling",
  year = 2012,
  journal = "BMC structural biology",
  publisher = "BioMed Central",
  volume = 12,
  number = 1,
  pages = "1-10"
}


@article{petukh2012predicting,
  author = "M. Petukh and M. Zhenirovskyy and C. Li and L. Li and L. Wang and E. Alexov",
  title = "Predicting nonspecific ion binding using DelPhi",
  year = 2012,
  journal = "Biophysical journal",
  publisher = "Elsevier",
  volume = 102,
  number = 12,
  pages = "2885-2893"
}


@article{li2012highly,
  author = "C. Li and L. Li and J. Zhang and E. Alexov",
  title = "Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi",
  year = 2012,
  journal = "Journal of computational chemistry",
  publisher = "Wiley Online Library",
  volume = 33,
  number = 24,
  pages = "1960-1966"
}


@article{smith2012delphi,
  author = "N. Smith and S. Witham and S. Sarkar and J. Zhang and L. Li and C. Li and E. Alexov",
  title = "DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol",
  year = 2012,
  journal = "Bioinformatics",
  publisher = "Oxford University Press",
  volume = 28,
  number = 12,
  pages = "1655-1657"
}


@article{zhang2012predicting,
  author = "Z. Zhang and L. Wang and Y. Gao and J. Zhang and M. Zhenirovskyy and E. Alexov",
  title = "Predicting folding free energy changes upon single point mutations",
  year = 2012,
  journal = "Bioinformatics",
  publisher = "Oxford University Press",
  volume = 28,
  number = 5,
  pages = "664-671"
}


@article{takano2012x,
  author = "K. Takano and D. Liu and P. Tarpey and E. Gallant and A. Lam and S. Witham and E. Alexov and A. Chaubey and R. E. Stevenson and C. E. Schwartz and others",
  title = "An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity",
  year = 2012,
  journal = "Human molecular genetics",
  publisher = "Oxford University Press",
  volume = 21,
  number = 20,
  pages = "4497-4507"
}


@article{zhang2012analyzing,
  author = "Z. Zhang and M. A. Miteva and L. Wang and E. Alexov",
  title = "Analyzing effects of naturally occurring missense mutations",
  year = 2012,
  journal = "Computational and mathematical methods in medicine",
  publisher = "Hindawi",
  volume = 2012
}


@article{li2012delphi,
  author = "L. Li and C. Li and S. Sarkar and J. Zhang and S. Witham and Z. Zhang and L. Wang and N. Smith and M. Petukh and E. Alexov",
  title = "DelPhi: a comprehensive suite for DelPhi software and associated resources",
  year = 2012,
  journal = "BMC biophysics",
  publisher = "BioMed Central",
  volume = 5,
  number = 1,
  pages = "1-11"
}


@article{quine2011discrete,
  author = "J. QUINE",
  title = "DISCRETE DIFFERENTIAL GEOMETRY OF CURVES AND PROTEIN STRUCTURE.",
  year = 2011
}


@article{zhang2011silico,
  author = "Z. Zhang and J. Norris and C. Schwartz and E. Alexov",
  title = "In Silico and In Vitro Investigations of the Mutability of Disease-Causing Missense Mutation Sites in",
  year = 2011
}


@inproceedings{zhang2011silico,
  author = "Z. Zhang and C. Schwatz and E. Alexov",
  title = "In silico investigation of molecular effects caused by missense mutations in creatine transporter protein",
  year = 2011,
  booktitle = "APS March Meeting Abstracts",
  volume = 2011,
  pages = "T39-002"
}


@inproceedings{wang2011using,
  author = "L. Wang and S. Sarhar and W. Rocchia and E. Alexov",
  title = "Using DelPhi capabilities to mimic conformational reorganization with amino acid specific dielectric constants",
  year = 2011,
  booktitle = "APS March Meeting Abstracts",
  volume = 2011,
  pages = "S1-156"
}


@article{zhang2011silico,
  author = "Z. Zhang and C. Schwartz and E. Alexov",
  title = "In Silico Investigation of Mutability of Spermine Synthase",
  year = 2011,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 100,
  number = 3,
  pages = "321a"
}


@article{zhang2011textit,
  author = "Z. Zhang and C. Schwatz and E. Alexov",
  title = "$\backslash$textit $\{$In silico$\}$ investigation of molecular effects caused by missense mutations in creatine transporter protein",
  year = 2011,
  journal = "Bulletin of the American Physical Society",
  publisher = "American Physical Society",
  volume = 56
}


@article{witham2011silico,
  author = "S. Witham and K. Takano and C. Schwartz and E. Alexov",
  title = "In Silico Investigation of a Missense Mutation in CLIC2 Associated with Intellectual Disability",
  year = 2011,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 100,
  number = 3,
  pages = "611a"
}


@inproceedings{witham2011delphi,
  author = "S. Witham and B. Boylen and B. Owesen and W. Rocchia and E. Alexov",
  title = "DelPhi webserver: Comprehensive suite for electrostatic calculations of biological macromolecules and their complexes",
  year = 2011,
  booktitle = "APS March Meeting Abstracts",
  volume = 2011,
  pages = "S1-155"
}


@article{witham2011developing,
  author = "S. Witham and K. Talley and L. Wang and Z. Zhang and S. Sarkar and D. Gao and W. Yang and E. Alexov",
  title = "Developing hybrid approaches to predict pKa values of ionizable groups",
  year = 2011,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  publisher = "Wiley Subscription Services, Inc., A Wiley Company Hoboken",
  volume = 79,
  number = 12,
  pages = "3389-3399"
}


@article{witham2011missense,
  author = "S. Witham and K. Takano and C. Schwartz and E. Alexov",
  title = "A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics",
  year = 2011,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  publisher = "Wiley Subscription Services, Inc., A Wiley Company Hoboken",
  volume = 79,
  number = 8,
  pages = "2444-2454"
}


@article{mitra2011silico,
  author = "R. C. Mitra and Z. Zhang and E. Alexov",
  title = "In silico modeling of pH-optimum of protein--protein binding",
  year = 2011,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  publisher = "Wiley Subscription Services, Inc., A Wiley Company Hoboken",
  volume = 79,
  number = 3,
  pages = "925-936"
}


@article{zhang2011silico,
  author = "Z. Zhang and J. Norris and C. Schwartz and E. Alexov",
  title = "In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in spermine synthase",
  year = 2011,
  journal = "PloS one",
  publisher = "Public Library of Science",
  volume = 6,
  number = 5,
  pages = "e20373"
}


@article{zhang2011role,
  author = "Z. Zhang and S. Witham and E. Alexov",
  title = "On the role of electrostatics in protein--protein interactions",
  year = 2011,
  journal = "Physical biology",
  publisher = "IOP Publishing",
  volume = 8,
  number = 3,
  pages = "035001"
}


@article{alexov2011progress,
  author = "E. Alexov and E. L. Mehler and N. Baker and A. M. Baptista and Y. Huang and F. Milletti and J. E. Nielsen and D. Farrell and T. Carstensen and M. H. Olsson and others",
  title = "Progress in the prediction of pKa values in proteins",
  year = 2011,
  journal = "Proteins: structure, function, and bioinformatics",
  publisher = "Wiley Subscription Services, Inc., A Wiley Company Hoboken",
  volume = 79,
  number = 12,
  pages = "3260-3275"
}


@article{chen2010quantum,
  author = "D. Chen and G.-W. Wei",
  title = "Quantum dynamics in continuum for proton channel transport",
  year = 2010
}


@article{zhe20102010,
  author = "Z. Zhe and T. Shaolei and E. Alexov",
  title = "From 2010 Abstracts Issue",
  year = 2010,
  journal = "Biophysical Journal",
  volume = 98,
  pages = "1096-1098"
}


@inproceedings{alexov2010structural,
  author = "E. Alexov and B. Honig",
  title = "Structural and Energetic Basis of Molecular Recognition",
  year = 2010,
  booktitle = "Handbook of Cell Signaling",
  publisher = "Academic Press",
  pages = "11-13"
}


@article{pittman2010pmcid,
  author = "A. Pittman and R. Saul and A. Chaubey and E. Alexov and M. Tiemeyer and R. Steet and C. Schwartz and M. B\'en\'eteau and J. Ricci and V. Desquiret-Dumas and others",
  title = "PMCID: PMC2695060.",
  year = 2010,
  journal = "Int Immunol",
  volume = 22,
  number = 7,
  pages = "593-603"
}


@article{zhe2010silico,
  author = "Z. Zhe and T. Shaolei and E. Alexov",
  title = "In Silico Investigation of the Molecular Effects Caused by Missense Mutations in Spermine Sythase Gene Associated with Human Mental Retardation",
  year = 2010,
  journal = "Biophysical Journal",
  publisher = "Elsevier",
  volume = 98,
  number = 3,
  pages = "571a"
}


@article{teng2010structural,
  author = "S. Teng and A. K. Srivastava and C. E. Schwartz and E. Alexov and L. Wang",
  title = "Structural assessment of the effects of Amino Acid Substitutions on protein stability and protein? protein interaction",
  year = 2010,
  journal = "International journal of computational biology and drug design",
  publisher = "Inderscience Publishers",
  volume = 3,
  number = 4,
  pages = "334-349"
}


@article{talley2010ph,
  author = "K. Talley and E. Alexov",
  title = "On the pH-optimum of activity and stability of proteins",
  year = 2010,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  publisher = "Wiley Subscription Services, Inc., A Wiley Company Hoboken",
  volume = 78,
  number = 12,
  pages = "2699-2706"
}


@article{zhang2010computational,
  author = "Z. Zhang and S. Teng and L. Wang and C. E. Schwartz and E. Alexov",
  title = "Computational analysis of missense mutations causing Snyder-Robinson syndrome",
  year = 2010,
  journal = "Human mutation",
  publisher = "Wiley Subscription Services, Inc., A Wiley Company Hoboken",
  volume = 31,
  number = 9,
  pages = "1043-1049"
}


@inproceedings{mitra2009modeling,
  author = "R. Mitra and R. Shyam and E. Alexov",
  title = "Modeling Ionization Events iduced by Protein Protein Binding",
  year = 2009,
  booktitle = "APS Southeastern Section Meeting Abstracts",
  volume = 76,
  pages = "PC-003"
}


@inproceedings{mitra2009multivariate,
  author = "I. Mitra and E. Alexov",
  title = "Multivariate Analysis of Conformational Changes Induced by Macromolecular Interactions",
  year = 2009,
  booktitle = "APS Southeastern Section Meeting Abstracts",
  volume = 76,
  pages = "PC-004"
}


@article{teng2009modeling,
  author = "S. Teng and T. Madej and A. Panchenko and E. Alexov",
  title = "Modeling effects of human single nucleotide polymorphisms on protein-protein interactions.(vol 96, pg 2178, 2009)",
  year = 2009,
  journal = "BIOPHYSICAL JOURNAL",
  publisher = "CELL PRESS 600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA",
  volume = 96,
  number = 11,
  pages = "4753-4753"
}


@inproceedings{shyam2009accessing,
  author = "R. Shyam and E. Alexov",
  title = "Accessing the limits of ab initio docking methods",
  year = 2009,
  booktitle = "APS Southeastern Section Meeting Abstracts",
  volume = 76,
  pages = "PC-002"
}


@inproceedings{zhang2009computational,
  author = "Z. Zhang and S. Teng and E. Alexov",
  title = "Computational Modeling of Molecular Effects of Mutations Causing Snyder-Robinson Syndrome",
  year = 2009,
  booktitle = "APS Southeastern Section Meeting Abstracts",
  volume = 76,
  pages = "PC-007"
}


@article{teng2009modeling,
  author = "S. Teng and T. Madej and A. Panchenko and E. Alexov",
  title = "Modeling effects of human single nucleotide polymorphisms on protein-protein interactions",
  year = 2009,
  journal = "Biophysical journal",
  publisher = "Elsevier",
  volume = 96,
  number = 6,
  pages = "2178-2188"
}


@article{alexov2008editorial,
  author = "E. Alexov",
  title = "Editorial [Protein-Protein Interactions Guest Editor: Emil Alexov]",
  year = 2008,
  journal = "Current pharmaceutical biotechnology",
  publisher = "Bentham Science Publishers",
  volume = 9,
  number = 2,
  pages = "55-56"
}


@article{talley2008modeling,
  author = "K. Talley and P. Kundrotas and E. Alexov",
  title = "Modeling salt dependence of protein-protein association: Linear vs non-linear Poisson-Boltzmann equation",
  year = 2008,
  journal = "Commun Comput Phys",
  volume = 3,
  number = 5,
  pages = "1071-1086"
}


@article{mitra2008calculating,
  author = "R. Mitra and R. Shyam and I. Mitra and M. A. Miteva and E. Alexov",
  title = "Calculating the protonation states of proteins and small molecules: Implications to ligand-receptor interactions",
  year = 2008,
  journal = "Current computer-aided drug design",
  publisher = "Bentham Science Publishers",
  volume = 4,
  number = 3,
  pages = "169-179"
}


@article{kosloff2008electrostatic,
  author = "M. Kosloff and E. Alexov and V. Y. Arshavsky and B. Honig",
  title = "Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation",
  year = 2008,
  journal = "Journal of Biological Chemistry",
  publisher = "Elsevier",
  volume = 283,
  number = 45,
  pages = "31197-31207"
}


@article{talley2008electrostatic,
  author = "K. Talley and C. Ng and M. Shoppell and P. Kundrotas and E. Alexov",
  title = "On the electrostatic component of protein-protein binding free energy",
  year = 2008,
  journal = "PMC biophysics",
  publisher = "BioMed Central",
  volume = 1,
  number = 1,
  pages = "1-23"
}


@article{kundrotas2008homology,
  author = "P. J. Kundrotas and M. F. Lensink and E. Alexov",
  title = "Homology-based modeling of 3D structures of protein--protein complexes using alignments of modified sequence profiles",
  year = 2008,
  journal = "International journal of biological macromolecules",
  publisher = "Elsevier",
  volume = 43,
  number = 2,
  pages = "198-208"
}


@article{teng2008approaches,
  author = "S. Teng and E. Michonova-Alexova and E. Alexov",
  title = "Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions",
  year = 2008,
  journal = "Current pharmaceutical biotechnology",
  publisher = "Bentham Science Publishers",
  volume = 9,
  number = 2,
  pages = "123-133"
}


@inproceedings{alexov2007optimization,
  author = "E. Alexov and K. Brock and P. Kundrotas",
  title = "Optimization of the electrostatic interactions in protein-protein complexes",
  year = 2007,
  booktitle = "APS March Meeting Abstracts",
  pages = "K1-021"
}


@article{smith2007strategies,
  author = "S. Smith and L. Bost",
  title = "Strategies For Increasing Response Rates",
  year = 2007,
  journal = "National Dropout Prevention Center for Students with Disabilities, Oregon"
}


@inproceedings{alexov2007modeling,
  author = "E. G. Alexov",
  title = "Modeling protein-protein interactions with continuum electrostatics",
  year = 2007,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 233,
  pages = "52-52"
}


@inproceedings{kundrotas2007utilizing,
  author = "P. Kundrotas and E. Alexov",
  title = "Utilizing Profile-to-Profile Alignments for Predicting Protein-Protein Interactions",
  year = 2007,
  booktitle = "APS March Meeting Abstracts",
  pages = "K1-020"
}


@inproceedings{kundrotas2007predicting,
  author = "P. Kundrotas and E. Alexov",
  title = "Predicting protein-protein interactions using non-gapped interacting residue segments",
  year = 2007,
  booktitle = "BIOPHYSICAL JOURNAL",
  pages = "367A-368A"
}


@article{kundrotas2007banmoki,
  author = "P. Kundrotas and P. Georgieva and A. Shosheva and P. Christova and E. Alexov",
  title = "BANMOKI: A searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families",
  year = 2007,
  journal = "International journal of biological macromolecules",
  publisher = "Elsevier",
  volume = 41,
  number = 1,
  pages = "114-119"
}


@article{miteva2007protein,
  author = "M. A. Miteva and E. Alexov and B. O. Villoutreix",
  title = "Protein Structure Analysis Online",
  year = 2007,
  journal = "Current protocols in protein science",
  volume = 50,
  number = 1,
  pages = "2-13"
}


@article{kundrotas2007predicting,
  author = "P. Kundrotas and E. Alexov",
  title = "Predicting interacting and interfacial residues using continuous sequence segments",
  year = 2007,
  journal = "International journal of biological macromolecules",
  publisher = "Elsevier",
  volume = 41,
  number = 5,
  pages = "615-623"
}


@article{kundrotas2007assessing,
  author = "P. Kundrotas and P. Georgieva and A. Shosheva and P. Christova and E. Alexov",
  title = "Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families",
  year = 2007,
  journal = "Journal of bioinformatics and computational biology",
  publisher = "World Scientific",
  volume = 5,
  number = 3,
  pages = "693-715"
}


@article{isvoran2007electrostatic,
  author = "A. Isvoran and C. Craescu and E. Alexov",
  title = "Electrostatic control of the overall shape of calmodulin: numerical calculations",
  year = 2007,
  journal = "European Biophysics Journal",
  publisher = "Springer-Verlag",
  volume = 36,
  number = 3,
  pages = "225-237"
}


@article{ofiteru2007structural,
  author = "A. Ofiteru and N. Bucurenci and E. Alexov and T. Bertrand and P. Briozzo and H. Munier-Lehmann and A.-M. Gilles",
  title = "Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase",
  year = 2007,
  journal = "The FEBS journal",
  publisher = "Blackwell Publishing Ltd Oxford, UK",
  volume = 274,
  number = 13,
  pages = "3363-3373"
}


@article{brock2007optimization,
  author = "K. Brock and K. Talley and K. Coley and P. Kundrotas and E. Alexov",
  title = "Optimization of electrostatic interactions in protein-protein complexes",
  year = 2007,
  journal = "Biophysical journal",
  publisher = "Elsevier",
  volume = 93,
  number = 10,
  pages = "3340-3352"
}


@article{kundrotas2007protcom,
  author = "P. J. Kundrotas and E. Alexov",
  title = "PROTCOM: searchable database of protein complexes enhanced with domain--domain structures",
  year = 2007,
  journal = "Nucleic Acids Research",
  publisher = "Oxford University Press",
  volume = 35,
  number = 1,
  pages = "D575-D579"
}


@article{bertonati2007poisson,
  author = "C. Bertonati and B. Honig and E. Alexov",
  title = "Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies",
  year = 2007,
  journal = "Biophysical journal",
  publisher = "Elsevier",
  volume = 92,
  number = 6,
  pages = "1891-1899"
}


@article{tang2007calculation,
  author = "C. L. Tang and E. Alexov and A. M. Pyle and B. Honig",
  title = "Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides",
  year = 2007,
  journal = "Journal of molecular biology",
  publisher = "Academic Press",
  volume = 366,
  number = 5,
  pages = "1475-1496"
}


@inproceedings{kundrotas2006optimum,
  author = "P. Kundrotas and E. Alexov",
  title = "Optimum pH for protein-protein complexes.",
  year = 2006,
  booktitle = "APS March Meeting Abstracts",
  pages = "C1-121"
}


@inproceedings{alexov2006combining,
  author = "E. Alexov and A. Allardice and P. Kundrotas",
  title = "Combining biophysical and bioinformatical approaches for predicting residue's contacts.",
  year = 2006,
  booktitle = "APS March Meeting Abstracts",
  pages = "A26-014"
}


@inproceedings{kundrotas2006predicting,
  author = "P. Kundrotas and E. Alexov",
  title = "Predicting 3D structures of transient protein-protein complexes",
  year = 2006,
  booktitle = "APS March Meeting Abstracts",
  pages = "A26-007"
}


@article{kundrotas2006predicting,
  author = "P. J. Kundrotas and E. Alexov",
  title = "Predicting 3D structures of transient protein--protein complexes by homology",
  year = 2006,
  journal = "Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics",
  publisher = "Elsevier",
  volume = 1764,
  number = 9,
  pages = "1498-1511"
}


@article{kundrotas2006predicting,
  author = "P. J. Kundrotas and E. G. Alexov",
  title = "Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives",
  year = 2006,
  journal = "BMC bioinformatics",
  publisher = "BioMed Central",
  volume = 7,
  number = 1,
  pages = "1-9"
}


@article{kundrotas2006electrostatic,
  author = "P. J. Kundrotas and E. Alexov",
  title = "Electrostatic properties of protein-protein complexes",
  year = 2006,
  journal = "Biophysical journal",
  publisher = "Elsevier",
  volume = 91,
  number = 5,
  pages = "1724-1736"
}


@article{grey2006characterizing,
  author = "M. J. Grey and Y. Tang and E. Alexov and C. J. McKnight and D. P. Raleigh and A. G. Palmer III",
  title = "Characterizing a partially folded intermediate of the villin headpiece domain under non-denaturing conditions: contribution of His41 to the pH-dependent stability of the N-terminal subdomain",
  year = 2006,
  journal = "Journal of molecular biology",
  publisher = "Academic Press",
  volume = 355,
  number = 5,
  pages = "1078-1094"
}


@article{wu2006coating,
  author = "Y. Wu and J. S. Hudson and Q. Lu and J. M. Moore and A. S. Mount and A. M. Rao and E. Alexov and P. C. Ke",
  title = "Coating single-walled carbon nanotubes with phospholipids",
  year = 2006,
  journal = "The Journal of Physical Chemistry B",
  publisher = "American Chemical Society",
  volume = 110,
  number = 6,
  pages = "2475-2478"
}


@article{shosheva2005comparative,
  author = "A. Shosheva and A. Donchev and M. Dimitrov and G. Kostov and G. Toromanov and V. Getov and E. Alexov",
  title = "Comparative study of the stability of poplar plastocyanin isoforms",
  year = 2005,
  journal = "Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics",
  publisher = "Elsevier",
  volume = 1748,
  number = 1,
  pages = "116-127"
}


@article{zhu2005comparative,
  author = "J. Zhu and E. Alexov and B. Honig",
  title = "Comparative study of generalized Born models: Born radii and peptide folding",
  year = 2005,
  journal = "The Journal of Physical Chemistry B",
  publisher = "ACS Publications",
  volume = 109,
  number = 7,
  pages = "3008-3022"
}


@article{tanaka1748proteins,
  author = "N. Tanaka and S. Nakao and J. Chatellier and Y. Tani and T. Tada and S. Kunugi and F. Sicilia and B. Mattei and F. Cervone and D. Bellincampi and others",
  title = "Proteins and Proteomics Cumulative Contents",
  year = 2005,
  journal = "Biochimica et Biophysica Acta",
  volume = 1748,
  pages = "233-234"
}


@article{alexov2004modeling,
  author = "E. Alexov and M. Gunner",
  title = "Modeling the First Electron Transfer from QA to QB",
  year = 2004,
  journal = "Molecular Bioenergetics: Simulations of Electron, Proton, and Energy Transfer",
  publisher = "Amer Chemical Society",
  number = 883,
  pages = "93"
}


@inproceedings{alexov2004modeling,
  author = "E. Alexov and M. Gunner",
  title = "Modeling the First Electron Transfer from QA to QB in Reaction Center Proteins from Rb. sphaeroides",
  year = 2004
}


@inproceedings{tang2004use,
  author = "C. L. Tang and D. Petrey and M. Fasnacht and M. Kosloff and E. Alexov and B. Honig",
  title = "Use of limited suboptimal alignment in homology modeling",
  year = 2004,
  booktitle = "Poster presented at 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB)"
}


@article{shosheva2004experimental,
  author = "A. Shosheva and A. Donchev and M. Dimitrov and I. Zlatanov and G. Toromanov and V. Getov and E. Alexov",
  title = "Experimental and numerical study of the poplar plastocyanin isoforms using Tyr as a probe for electrostatic similarity and dissimilarity",
  year = 2004,
  journal = "Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics",
  publisher = "Elsevier",
  volume = 1698,
  number = 1,
  pages = "67-75"
}


@article{alexov2004calculating,
  author = "E. Alexov",
  title = "Calculating proton uptake/release and binding free energy taking into account ionization and conformation changes induced by protein--inhibitor association: application to plasmepsin, cathepsin D and endothiapepsin--pepstatin complexes",
  year = 2004,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  publisher = "Wiley Online Library",
  volume = 56,
  number = 3,
  pages = "572-584"
}


@article{alexov2004numerical,
  author = "E. Alexov",
  title = "Numerical calculations of the pH of maximal protein stability: The effect of the sequence composition and three-dimensional structure",
  year = 2004,
  journal = "European Journal of Biochemistry",
  publisher = "Blackwell Science Ltd Oxford, UK",
  volume = 271,
  number = 1,
  pages = "173-185"
}


@inproceedings{alexov2003proton,
  author = "E. Alexov and B. Honig",
  title = "Proton uptake/release induced by protein-inhibitor association. Application to pepstatin and plasmepsin, cathepsin D and endothiapepsin complexes.",
  year = 2003,
  booktitle = "BIOPHYSICAL JOURNAL",
  volume = 84,
  number = 2,
  pages = "505A-505A"
}


@article{alexov2003role,
  author = "E. Alexov",
  title = "Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: Comparing experimental with computed pKas",
  year = 2003,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  publisher = "Wiley Online Library",
  volume = 50,
  number = 1,
  pages = "94-103"
}


@article{tang2003role,
  author = "C. L. Tang and L. Xie and I. Y. Koh and S. Posy and E. Alexov and B. Honig",
  title = "On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles",
  year = 2003,
  journal = "Journal of molecular biology",
  publisher = "Elsevier",
  volume = 334,
  number = 5,
  pages = "1043-1062"
}


@article{petrey2003using,
  author = "D. Petrey and Z. Xiang and C. L. Tang and L. Xie and M. Gimpelev and T. Mitros and C. S. Soto and S. Goldsmith-Fischman and A. Kernytsky and A. Schlessinger and others",
  title = "Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling",
  year = 2003,
  journal = "Proteins: Structure, Function, and Bioinformatics",
  publisher = "Wiley Subscription Services, Inc., A Wiley Company Hoboken",
  volume = 53,
  number = 6,
  pages = "430-435"
}


@article{rocchia2002rapid,
  author = "W. Rocchia and S. Sridharan and A. Nicholls and E. Alexov and A. Chiabrera and B. Honig",
  title = "Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method",
  year = 2002,
  journal = "J Comp Chem",
  volume = 23,
  pages = "128-137"
}


@inproceedings{tang2002perturbations,
  author = "C. Tang and E. Alexov and A. Pyle and B. Honig",
  title = "Perturbations of pKa in RNA structures: A survey using a Monte Carlo application of the NLPB equation",
  year = 2002,
  booktitle = "BIOPHYSICAL JOURNAL",
  volume = 82,
  number = 1,
  pages = "131A-131A"
}


@inproceedings{alexov2002origins,
  author = "E. Alexov and B. Honig",
  title = "The origins of pH dependent effects on protein stability: Applications to proteases",
  year = 2002,
  booktitle = "Biophysical Journal",
  volume = 82,
  number = 1,
  pages = "474A-474A"
}


@article{tandori2002key,
  author = "J. Tandori and P. Maroti and E. Alexov and P. Sebban and L. Baciou",
  title = "Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides",
  year = 2002,
  journal = "Proceedings of the National Academy of Sciences",
  publisher = "National Academy of Sciences",
  volume = 99,
  number = 10,
  pages = "6702-6706"
}


@article{georgescu2002combining,
  author = "R. E. Georgescu and E. G. Alexov and M. R. Gunner",
  title = "Combining conformational flexibility and continuum electrostatics for calculating pKas in proteins",
  year = 2002,
  journal = "Biophysical journal",
  publisher = "Cell Press",
  volume = 83,
  number = 4,
  pages = "1731-1748"
}


@article{rocchia2002rapid,
  author = "W. Rocchia and S. Sridharan and A. Nicholls and E. Alexov and A. Chiabrera and B. Honig",
  title = "Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects",
  year = 2002,
  journal = "Journal of computational chemistry",
  publisher = "Wiley Online Library",
  volume = 23,
  number = 1,
  pages = "128-137"
}


@article{rocchia2001extending,
  author = "W. Rocchia and E. Alexov and B. Honig",
  title = "Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions (vol 105B, pg 6507, 2001)",
  year = 2001,
  journal = "Journal of Physical Chemistry B",
  publisher = "American Chemical Society (ACS)",
  volume = 105,
  number = 28,
  pages = "6754-6754"
}


@article{tandori2001accelerated,
  author = "J. Tandori and L. Baciou and E. Alexov and P. Maroti and M. Schiffer and D. K. Hanson and P. Sebban",
  title = "ACCELERATED PUBLICATIONS-Revealing the involvement of extended hydrogen bond networks in the cooperative function between distant sites in bacterial reaction centers.",
  year = 2001,
  journal = "Journal of Biological Chemistry",
  publisher = "Baltimore [etc.]",
  volume = 276,
  number = 49,
  pages = "45513-45515"
}


@article{rocchia2001additions,
  author = "W. Rocchia and E. Alexov and B. Honig",
  title = "ADDITIONS AND CORRECTIONS-Extending the Applicability of the Nonlinear Poisson-Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions",
  year = 2001,
  journal = "Journal of Physical Chemistry B-Condensed Phase",
  publisher = "Washington, DC: American Chemical Society, c1997-",
  volume = 105,
  number = 28,
  pages = "6754"
}


@article{tandori2001revealing,
  author = "J. Tandori and L. Baciou and E. Alexov and P. Mar\'oti and M. Schiffer and D. K. Hanson and P. Sebban",
  title = "Revealing the involvement of extended hydrogen bond networks in the cooperative function between distant sites in bacterial reaction centers",
  year = 2001,
  journal = "Journal of Biological Chemistry",
  publisher = "Elsevier",
  volume = 276,
  number = 49,
  pages = "45513-45515"
}


@article{rocchia2001extending,
  author = "W. Rocchia and E. Alexov and B. Honig",
  title = "Extending the applicability of the nonlinear Poisson- Boltzmann equation: multiple dielectric constants and multivalent ions",
  year = 2001,
  journal = "The Journal of Physical Chemistry B",
  publisher = "American Chemical Society",
  volume = 105,
  number = 28,
  pages = "6507-6514"
}


@inproceedings{alexov2000modeling,
  author = "E. Alexov and L. Baciou and M. Schiffer and P. Sebban and D. Hanson and M. Gunner",
  title = "Modeling the free energy chances due to mutations of residues with multi conformation continuum electrostatic (MCCE) method: Application to reaction center proteins",
  year = 2000,
  booktitle = "BIOPHYSICAL JOURNAL",
  volume = 78,
  number = 1,
  pages = "31A-31A"
}


@inproceedings{gunner2000calculating,
  author = "M. Gunner and E. Alexov",
  title = "Calculating the role of the protein in proton-and electron-transfer reactions.",
  year = 2000,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 219,
  pages = "U346-U346"
}


@inproceedings{gunner2000reorganization,
  author = "M. Gunner and E. Alexov",
  title = "Reorganization of the QB pocket of photosynthetic reaction centers stabilizes ionization changes.",
  year = 2000,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 220,
  pages = "U186-U186"
}


@inproceedings{gunner2000pk,
  author = "M. Gunner and D. Karpman and E. Alexov",
  title = "pK (a) calculations with conformational flexibility: the multi conformation continuum electrostatics procedure (MCCE)",
  year = 2000,
  booktitle = "Biophysical Journal",
  volume = 78,
  number = 1,
  pages = "31A-31A"
}


@article{alexov2000modeling,
  author = "E. Alexov and J. Miksovska and L. Baciou and M. Schiffer and D. Hanson and P. Sebban and M. Gunner",
  title = "Modeling the effects of mutations on the free energy of the first electron transfer from QA-to QB in photosynthetic reaction centers",
  year = 2000,
  journal = "Biochemistry",
  publisher = "ACS Publications",
  volume = 39,
  number = 20,
  pages = "5940-5952"
}


@article{gunner2000pragmatic,
  author = "M. Gunner and E. Alexov",
  title = "A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins",
  year = 2000,
  journal = "Biochimica et Biophysica Acta (BBA)-Bioenergetics",
  publisher = "Elsevier",
  volume = 1458,
  number = 1,
  pages = "63-87"
}


@inproceedings{alexov1999modeling,
  author = "E. Alexov and M. Gunner",
  title = "Modeling the first electron transfer from QA to QB in reaction centers from the bacteria Rb.",
  year = 1999,
  booktitle = "Biophysical Journal",
  volume = 76,
  number = 1,
  pages = "A240-A240"
}


@article{alexov1999calculated,
  author = "E. Alexov and M. Gunner",
  title = "Calculated protein and proton motions coupled to electron transfer: electron transfer from QA-to QB in bacterial photosynthetic reaction centers",
  year = 1999,
  journal = "Biochemistry",
  publisher = "American Chemical Society",
  volume = 38,
  number = 26,
  pages = "8253-8270"
}


@inproceedings{gunner1998modeling,
  author = "M. Gunner and E. Alexov",
  title = "Modeling motions in protiens that are coupled to electron tranfers.",
  year = 1998,
  booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY",
  volume = 216,
  pages = "U159-U159"
}


@article{miteva1998numerical,
  author = "M. Miteva and E. Alexov and B. Atanasov",
  title = "Numerical simulation of aldolase tetramer stability",
  year = 1998,
  journal = "European biophysics journal",
  publisher = "Springer-Verlag",
  volume = 28,
  number = 1,
  pages = "67-73"
}


@inproceedings{gunner1997role,
  author = "M. R. Gunner and E. Alexov",
  title = "The Role of the Protein in Modulating Cofactor Electrochemistry in Proteins: The Calculation of Electrostatic Forces",
  year = 1997,
  booktitle = "Molecular Modeling and Dynamics of Bioinorganic Systems",
  publisher = "Springer, Dordrecht",
  pages = "361-390"
}


@article{gunner1997importance,
  author = "M. Gunner and E. Alexov and E. Torres and S. Lipovaca",
  title = "The importance of the protein in controlling the electrochemistry of heme metalloproteins: methods of calculation and analysis",
  year = 1997,
  journal = "JBIC Journal of Biological Inorganic Chemistry",
  publisher = "Springer-Verlag",
  volume = 2,
  number = 1,
  pages = "126-134"
}


@article{alexov1997incorporating,
  author = "E. Alexov and M. Gunner",
  title = "Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties",
  year = 1997,
  journal = "Biophysical journal",
  publisher = "Cell Press",
  volume = 72,
  number = 5,
  pages = "2075-2093"
}


@article{ohshima1996electrostatic,
  author = "H. Ohshima and E. Mishonova and E. Alexov",
  title = "Electrostatic interaction between two charged spherical molecules",
  year = 1996,
  journal = "Biophysical chemistry",
  publisher = "Elsevier",
  volume = 57,
  number = 23,
  pages = "189-203"
}


@inproceedings{alexandrov1995participant,
  author = "V. Alexandrov and E. G. Alexov and M. Andrec and A. Apostolico and A. Bhattacharya and D. J. Brooks and R. L. Cai and A. Colasanti and W. Ding and P. Du and others",
  title = "Participant List",
  year = 1995,
  booktitle = "Proceedings of the Tsukuba Global Carbon Cycle Workshop--Global Environment Tsukuba'95: February 1-3, 1995, Tsukuba, Japan",
  pages = "169"
}


@article{alexov1995anisotropic,
  author = "E. Alexov and B. Atanasov and T. Ueki",
  title = "Anisotropic behavior of the pH dependence part of Young's modulus in a lysozyme triclinic crystal",
  year = 1995,
  journal = "Biopolymers: Original Research on Biomolecules",
  publisher = "Wiley Subscription Services, Inc., A Wiley Company Hoboken",
  volume = 35,
  number = 5,
  pages = "513-522"
}


@article{alexov1995high,
  author = "E. Alexov",
  title = "High-Frequency Backward Waves in Longitudinally Magnetized Gyrotropic Waveguides",
  year = 1995,
  journal = "Contributions to Plasma Physics",
  publisher = "WILEY-VCH Verlag Berlin",
  volume = 35,
  number = 1,
  pages = "23-32"
}


@article{alexov1995selective,
  author = "E. Alexov and B. Atanasov",
  title = "Selective absorption of radio frequency energy due to collective motion of charged domains: case of lysozyme crystal",
  year = 1995,
  journal = "Journal of Biomolecular Structure and Dynamics",
  publisher = "Taylor \& Francis Group",
  volume = 13,
  number = 2,
  pages = "219-228"
}


@article{ivanov1994cherenkov,
  author = "S. Ivanov and E. Alexov",
  title = "Cherenkov generation of Rayleigh electromagnetic wave in a gyrotropic plasma waveguide",
  year = 1994,
  journal = "Nuclear Instruments and Methods in Physics Research A",
  volume = 341,
  number = 1,
  pages = "ABS109-ABS110"
}


@article{alexov1994modeling,
  author = "E. Alexov and E. Mishonova",
  title = "Modeling of the electrostatic potential created by a spherical molecule",
  year = 1994,
  journal = "Journal of Macromolecular Science, Part B",
  publisher = "Taylor \& Francis Group",
  volume = 33,
  number = 1,
  pages = "21-35"
}


@article{alexov1994analysis,
  author = "E. Alexov and B. Atanasov",
  title = "Analysis of electrostatic interactions in ribonuclease A monoclinic crystal",
  year = 1994,
  journal = "Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology",
  publisher = "Elsevier",
  volume = 1206,
  number = 1,
  pages = "55-62"
}


@article{alexov1994rejection,
  author = "E. G. Alexov and S. T. Ivanov and M. I. Kapchinskii",
  title = "Rejection band in waveguide filled with cold magnetoactive plasma",
  year = 1994,
  journal = "Japanese journal of applied physics",
  publisher = "IOP Publishing",
  volume = 33,
  number = 5,
  pages = "2730"
}


@article{ivanov1994polaritons,
  author = "S. T. Ivanov and K. Ivanova and E. Alexov",
  title = "Polaritons along the interface between an anisotropic semiconductor and a metallic screen",
  year = 1994,
  journal = "Physica Scripta",
  publisher = "IOP Publishing",
  volume = 49,
  number = 2,
  pages = "228"
}


@article{ivanov1993rayleigh,
  author = "S. Ivanov and K. Ivanova and E. Alexov",
  title = "Rayleigh surface waves along the boundary between a plasma and a metallic screen",
  year = 1993,
  journal = "Journal of plasma physics",
  publisher = "Cambridge University Press",
  volume = 49,
  number = 2,
  pages = "227-235"
}


@article{alexov1993nonreciprocal,
  author = "E. G. Alexov and S. T. Ivanov",
  title = "Nonreciprocal effects in a plasma waveguide",
  year = 1993,
  journal = "IEEE transactions on plasma science",
  publisher = "IEEE",
  volume = 21,
  number = 2,
  pages = "254-257"
}


@article{alexov1992additional,
  author = "E. Alexov",
  title = "An additional solution of the waveguide problem for a waveguide partially filled with a magnetoactive semiconductor plasma",
  year = 1992,
  journal = "Physica Scripta",
  publisher = "IOP Publishing",
  volume = 46,
  number = 5,
  pages = "429"
}


@article{alexov1990anisotropic,
  author = "E. Alexov and S. Ivanov",
  title = "Anisotropic TEM-mode in a plasma waveguide",
  year = 1990,
  journal = "Sov. J. Plasma Phys.(USA)",
  volume = 16,
  pages = "283"
}


@article{ivanov1990surface,
  author = "S. Ivanov and E. Alexov and A. Bogdanov and P. Malinov",
  title = "Surface wave evolution in a waveguide with an axial plasma column upon changing the external magnetic field",
  year = 1990,
  journal = "Plasma physics and controlled fusion",
  publisher = "IOP Publishing",
  volume = 32,
  number = 10,
  pages = "791"
}


@article{ivanov1990electromagnetic,
  author = "S. Ivanov and E. Alexov",
  title = "Electromagnetic waves in waveguide partially filled with semiconductor plasma",
  year = 1990,
  journal = "Contributions to Plasma Physics",
  publisher = "WILEY-VCH Verlag Berlin",
  volume = 30,
  number = 6,
  pages = "763-774"
}


@article{ivanov1990waveguide,
  author = "S. Ivanov and E. Alexov and P. Malinov",
  title = "Waveguide partially filled with semiconductor plasma",
  year = 1990,
  journal = "Physica Scripta",
  publisher = "IOP Publishing",
  volume = 42,
  number = 4,
  pages = "452"
}


@article{ivanov1990nonsymmetrical,
  author = "S. Ivanov and E. Alexov and P. Malinov",
  title = "Nonsymmetrical Electromagnetic Waves in Partially Plasma—Filled Waveguide",
  year = 1990,
  journal = "Contributions to Plasma Physics",
  publisher = "WILEY-VCH Verlag Berlin",
  volume = 30,
  number = 6,
  pages = "755-762"
}


@article{ivanov1990new,
  author = "S. Ivanov and A. Bogdanov and E. Alexov",
  title = "A new family of electromagnetic waves in a waveguide filled with magnetoactive semiconductor plasma",
  year = 1990,
  journal = "Physica Scripta",
  publisher = "IOP Publishing",
  volume = 42,
  number = 4,
  pages = "458"
}


@article{ivanov1990electromagnetic,
  author = "S. Ivanov and E. Alexov",
  title = "Electromagnetic waves in a plasma waveguide",
  year = 1990,
  journal = "Journal of plasma Physics",
  publisher = "Cambridge University Press",
  volume = 43,
  number = 1,
  pages = "51-67"
}


@article{ivanov1989electromagnetic,
  author = "S. Ivanov and E. Alexov",
  title = "Electromagnetic waven in fully-filled plasma waveguide",
  year = 1989,
  journal = "J. of Plasma",
  volume = 15,
  pages = "1131-1131"
}


@article{ivanov1989cyclotron,
  author = "S. Ivanov and E. G. Aleksov",
  title = "Cyclotron waves in a plasma waveguide",
  year = 1989,
  journal = "Fizika Plazmy",
  volume = 15,
  number = 9,
  pages = "1131-1134"
}


@article{ivanov1989electromagnetic,
  author = "S. Ivanov and E. Alexov",
  title = "Electromagnetic waves in the semiconductor plasma waveguide",
  year = 1989,
  journal = "Physica Scripta",
  publisher = "IOP Publishing",
  volume = 40,
  number = 1,
  pages = "58"
}


@article{ivanov1989symmetrical,
  author = "S. Ivanov and E. Alexov and P. Malinov",
  title = "Symmetrical electromagnetic waves in partially-filled plasma waveguide",
  year = 1989,
  journal = "Plasma physics and controlled fusion",
  publisher = "IOP Publishing",
  volume = 31,
  number = 6,
  pages = "941"
}