TY - JOUR T1 - Convergence of a diffuse interface Poisson-Boltzmann (pb) model to the sharp interface pb model: a unified regularization formulation AU - Shao, Y. AU - McGowan, M. AU - Wang, S. AU - Alexov, E. AU - Zhao, S. JO - Applied Mathematics and Computation PY - 2023 VL - 436 SP - 127501 EP - 127501 ER - TY - JOUR T1 - Electrostatics in Computational Biophysics and Its Implications for Disease Effects AU - Sun, S. AU - Poudel, P. AU - Alexov, E. AU - Li, L. JO - International Journal of Molecular Sciences PY - 2022 VL - 23 IS - 18 SP - 10347 EP - 10347 ER - TY - JOUR T1 - Protein–Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation AU - Panday, S. AU - Alexov, E. JO - ACS omega PY - 2022 VL - 7 IS - 13 SP - 11057 EP - 11067 ER - TY - JOUR T1 - A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions AU - Wang, S. AU - Shao, Y. AU - Alexov, E. AU - Zhao, S. JO - Journal of Computational Physics PY - 2022 SP - 111340 EP - 111340 ER - TY - JOUR T1 - Increased p53 signaling impairs neural differentiation causing HUWE1-promoted intellectual disabilities AU - Aprigliano, R. AU - Bradamante, S. AU - Mihaljevic, B. AU - Wang, W. AU - Martin, S. L. F. AU - Bordin, D. L. AU - Bosshard, M. AU - Montaldo, N. P. AU - Peng, Y. AU - Alexov, E. AU - others, JO - Cell Reports Medicine PY - 2021 PB - Cold Spring Harbor Laboratory VL - 2 SP - 100240 EP - 100240 M3 - doi:https://doi.org/10.1016/j.xcrm.2021.100240 UR - https://www.cell.com/cell-reports-medicine/pdf/S2666-3791(21)00056-2.pdf ER - TY - JOUR T1 - Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease AU - Koirala, M. AU - Shashikala, H. AU - Jeffries, J. AU - Wu, B. AU - Loftus, S. K. AU - Zippin, J. H. AU - Alexov, E. JO - International journal of molecular sciences PY - 2021 PB - Multidisciplinary Digital Publishing Institute VL - 22 IS - 15 SP - 8273 EP - 8273 ER - TY - JOUR T1 - Special Issue on Computational Chemistry Methods to Predict pKa’s of Ionizable Groups in Proteins, RNAs, DNAs and Small Molecules AU - Alexov, E. JO - Journal of Computational Biophysics and Chemistry PY - 2021 VL - 20 IS - 2 SP - 109 EP - 110 ER - TY - JOUR T1 - SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions. AU - Li, G. AU - Panday, S. AU - Peng, Y. AU - Alexov, E. JO - Bioinformatics (Oxford, England) PY - 2021 ER - TY - JOUR T1 - Opioid Addiction and Opioid Receptor Dimerization: Structural Modeling of the OPRD1 and OPRM1 Heterodimer and Its Signaling Pathways. AU - Wu, B. AU - Hand, W. AU - Alexov, E. JO - International journal of molecular sciences PY - 2021 PB - Multidisciplinary Digital Publishing Institute (MDPI) VL - 22 IS - 19 ER - TY - JOUR T1 - On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary [J] AU - Wang, S. AU - Alexov, E. AU - Zhao, S. JO - Mathematical Biosciences and Engineering PY - 2021 VL - 18 IS - 2 SP - 1370 EP - 1405 ER - TY - JOUR T1 - SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability AU - Li, G. AU - Panday, S. K. AU - Alexov, E. JO - International Journal of Molecular Sciences PY - 2021 PB - Multidisciplinary Digital Publishing Institute VL - 22 IS - 2 SP - 606 EP - 606 ER - TY - JOUR T1 - BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics AU - Shashikala, H. AU - Chakravorty, A. AU - Panday, S. K. AU - Alexov, E. JO - International Journal of Molecular Sciences PY - 2021 PB - Multidisciplinary Digital Publishing Institute VL - 22 IS - 1 SP - 272 EP - 272 ER - TY - JOUR T1 - Opioid addiction and opioid receptor dimerization: structural modeling of the OPRD1 and OPRM1 heterodimer and its signaling pathways AU - Wu, B. AU - Hand, W. AU - Alexov, E. JO - International journal of molecular sciences PY - 2021 VL - 22 IS - 19 SP - 10290 EP - 10290 ER - TY - JOUR T1 - SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions AU - Li, G. AU - Panday, S. AU - Peng, Y. AU - Alexov, E. JO - Bioinformatics PY - 2021 VL - 37 IS - 21 SP - 3760 EP - 3765 ER - TY - JOUR T1 - Special Issue on Computational Chemistry Methods to Predict pKa’s of Ionizable Groups in Proteins, RNAs, DNAs and Small Molecules AU - Alexov, E. JO - Journal of Computational Biophysics and Chemistry PY - 2021 VL - 2 IS - 2 SP - 109 EP - 110 M3 - doi:10.1142/S2737416521020014 UR - https://www.worldscientific.com/doi/10.1142/S2737416521020014 ER - TY - JOUR T1 - Towards More Biology-Oriented Papers: Name Change of the Journal of Theoretical and Computational Chemistry to Journal of Computational Biophysics and Chemistry AU - Alexov, E. JO - Journal of Computational Biophysics and Chemistry PY - 2021 PB - World Scientific Publishing Company VL - 20 IS - 1 SP - 1 EP - 1 M3 - doi:10.1142/S2737416521010018 ER - TY - JOUR T1 - An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants. AU - Alexov, E. AU - others, JO - Genes PY - 2020 VL - 11 IS - 9 ER - TY - JOUR T1 - A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation [J] AU - Li, C. AU - McGowan, M. AU - Alexov, E. AU - Zhao, S. JO - Mathematical Biosciences and Engineering PY - 2020 VL - 17 IS - 6 SP - 6259 EP - 6277 ER - TY - JOUR T1 - An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants AU - Ganakammal, S. R. AU - Alexov, E. JO - Genes PY - 2020 PB - Multidisciplinary Digital Publishing Institute VL - 11 IS - 9 SP - 1102 EP - 1102 ER - TY - JOUR T1 - SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein--protein binding affinity AU - Li, G. AU - Pahari, S. AU - Murthy, A. K. AU - Liang, S. AU - Fragoza, R. AU - Yu, H. AU - Alexov, E. JO - Bioinformatics PY - 2020 ER - TY - JOUR T1 - Ab-initio binding of barnase--barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach AU - Koirala, M. AU - Alexov, E. JO - Journal of Theoretical and Computational Chemistry PY - 2020 PB - World Scientific Publishing Company VL - 19 IS - 4 SP - 2050016 EP - 2050016 ER - TY - JOUR T1 - pH-dependent interactions of Apolipophorin-III with a lipid disk AU - Peng, Y. AU - Kelle, R. AU - Little, C. AU - Michonova, E. AU - Kornev, K. G. AU - Alexov, E. JO - Journal of Computational Biophysics and Chemistry PY - 2020 PB - World Scientific Publishing Company SP - 1 EP - 12 ER - TY - JOUR T1 - In-silico analysis to identify the role of MEN1 missense mutations in breast cancer AU - Ganakammal, S. R. AU - Koirala, M. AU - Wu, B. AU - Alexov, E. JO - Journal of Theoretical and Computational Chemistry PY - 2020 PB - World Scientific Publishing Company VL - 19 IS - 6 SP - 2041002 EP - 2041002 ER - TY - JOUR T1 - SAAMBE-3D: Predicting effect of mutations on protein--protein interactions AU - Pahari, S. AU - Li, G. AU - Murthy, A. K. AU - Liang, S. AU - Fragoza, R. AU - Yu, H. AU - Alexov, E. JO - International journal of molecular sciences PY - 2020 PB - Multidisciplinary Digital Publishing Institute VL - 21 IS - 7 SP - 2563 EP - 2563 ER - TY - JOUR T1 - Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi AU - Chakravorty, A. AU - Panday, S. AU - Pahari, S. AU - Zhao, S. AU - Alexov, E. JO - Journal of chemical information and modeling PY - 2020 PB - American Chemical Society VL - 60 IS - 4 SP - 2229 EP - 2246 ER - TY - JOUR T1 - Computational Analysis of Missense Mutations in Creatine Transporter Protein Associated with Creatine Deficiency Syndrome AU - Koirala, M. AU - Alexov, E. JO - Biophysical Journal PY - 2020 PB - Elsevier VL - 118 IS - 3 SP - 197a EP - 197a ER - TY - JOUR T1 - A regularization approach for solving Poisson’s equation with singular charge sources and diffuse interfaces AU - Wang, S. AU - Lee, A. AU - Alexov, E. AU - Zhao, S. JO - Applied Mathematics Letters PY - 2020 PB - Pergamon VL - 102 SP - 106144 EP - 106144 ER - TY - JOUR T1 - Computational chemistry methods to investigate the effects caused by DNA variants linked with disease AU - Koirala, M. AU - Alexov, E. JO - Journal of Theoretical and Computational Chemistry PY - 2020 PB - World Scientific Publishing Company VL - 19 IS - 6 SP - 1930001 EP - 1930001 ER - TY - CHAP T1 - Modeling pKa without solute-water boundary: DelPhiPKa and its applications to protein-protein binding AU - Pahari, S. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2019 VL - 258 ER - TY - CHAP T1 - Effect of water on the entropy of protein-protein binding AU - Chakravorty, A. AU - Higham, J. AU - Alexov, E. AU - Henchman, R. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2019 VL - 258 ER - TY - JOUR T1 - Reproducing ensemble averaged electrostatics with Super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes AU - Panday, S. K. AU - Shashikala, M. H. AU - Chakravorty, A. AU - Zhao, S. AU - Alexov, E. JO - Communications in Information and Systems PY - 2019 VL - 19 IS - 4 ER - TY - JOUR T1 - Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: Application to Rett syndrome variants AU - Ganakammal, S. R. AU - Alexov, E. JO - PeerJ PY - 2019 PB - PeerJ Inc. VL - 7 SP - e8106 EP - e8106 ER - TY - JOUR T1 - Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0] AU - Panday, S. K. AU - Shashikala, M. H. AU - Koirala, M. AU - Pahari, S. AU - Chakvorty, A. AU - Peng, Y. AU - Li, L. AU - Jia, Z. AU - Li, C. AU - Alexov, E. JO - Living Journal of Computational Molecular Science PY - 2019 PB - University of Colorado Boulder VL - 1 IS - 2 SP - 10841 EP - 10841 ER - TY - JOUR T1 - Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women AU - Wu, B. AU - Peng, Y. AU - Eggert, J. AU - Alexov, E. JO - International journal of molecular sciences PY - 2019 PB - Multidisciplinary Digital Publishing Institute VL - 20 IS - 19 SP - 4828 EP - 4828 ER - TY - JOUR T1 - Modeling electrostatic force in protein-protein recognition AU - Shashikala, H. AU - Chakravorty, A. AU - Alexov, E. JO - Frontiers in molecular biosciences PY - 2019 PB - Frontiers VL - 6 SP - 94 EP - 94 ER - TY - JOUR T1 - DFMD: fast and effective DelPhiForce steered molecular dynamics approach to model ligand approach toward a receptor: Application to spermine synthase enzyme AU - Peng, Y. AU - Yang, Y. AU - Li, L. AU - Jia, Z. AU - Cao, W. AU - Alexov, E. JO - Frontiers in molecular biosciences PY - 2019 PB - Frontiers VL - 6 SP - 74 EP - 74 ER - TY - JOUR T1 - Modeling pKas of unfolded proteins to probe structural models of unfolded state AU - Tajielyato, N. AU - Alexov, E. JO - Journal of Theoretical and Computational Chemistry PY - 2019 PB - World Scientific Publishing Company VL - 18 IS - 4 SP - 1950020 EP - 1950020 ER - TY - JOUR T1 - A super-Gaussian Poisson--Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states AU - Hazra, T. AU - Ullah, S. A. AU - Wang, S. AU - Alexov, E. AU - Zhao, S. JO - Journal of mathematical biology PY - 2019 PB - Springer Berlin Heidelberg VL - 79 IS - 2 SP - 631 EP - 672 ER - TY - JOUR T1 - Three additional patients with EED-associated overgrowth: potential mutation hotspots identified? AU - Spellicy, C. J. AU - Peng, Y. AU - Olewiler, L. AU - Cathey, S. S. AU - Rogers, R. C. AU - Bartholomew, D. AU - Johnson, J. AU - Alexov, E. AU - Lee, J. A. AU - Friez, M. J. AU - others, JO - Journal of human genetics PY - 2019 PB - Nature Publishing Group VL - 64 IS - 6 SP - 561 EP - 572 ER - TY - JOUR T1 - Processivity vs. beating: Comparing cytoplasmic and axonemal dynein microtubule binding domain association with microtubule AU - Tajielyato, N. AU - Alexov, E. JO - International journal of molecular sciences PY - 2019 PB - Multidisciplinary Digital Publishing Institute VL - 20 IS - 5 SP - 1090 EP - 1090 ER - TY - JOUR T1 - PKAD: a database of experimentally measured pKa values of ionizable groups in proteins AU - Pahari, S. AU - Sun, L. AU - Alexov, E. JO - Database PY - 2019 PB - Oxford Academic VL - 2019 ER - TY - JOUR T1 - Modeling Electrostatic Force in Protein-Protein Recognition AU - Bosthanthirige, M. S. H. AU - Chakravorty, A. AU - Alexov, E. JO - Biophysical Journal PY - 2019 PB - Elsevier VL - 116 IS - 3 SP - 46a EP - 46a ER - TY - JOUR T1 - New method to determine the effect of dimerization on protein flexibility from molecular dynamics simulation using structural hierarchy AU - Chakravorty, A. AU - Higham, J. AU - Alexov, E. AU - Henchman, R. H. JO - Biophysical Journal PY - 2019 PB - Elsevier VL - 116 IS - 3 SP - 561a EP - 562a ER - TY - JOUR T1 - Comparative Study of Flagellar and Cytoplasmic Dyneins AU - Tajielyato, N. AU - Alper, J. AU - Alexov, E. JO - Biophysical Journal PY - 2019 PB - Elsevier VL - 116 IS - 3 SP - 560a EP - 560a ER - TY - JOUR T1 - Surface-Free Protocol for Computing PKA's (DelPhiPKa): Applications to Protein-Protein Interactions AU - Pahari, S. AU - Sun, L. AU - Alexov, E. JO - Biophysical Journal PY - 2019 PB - Elsevier VL - 116 IS - 3 SP - 166a EP - 166a ER - TY - JOUR T1 - Investigating the Effects of Missense Mutations in MSH2 Gene Associated with Lynch Syndrome AU - Wu, B. AU - Peng, Y. AU - Eggert, J. A. AU - Alexov, E. JO - Biophysical Journal PY - 2019 PB - Elsevier VL - 116 IS - 3 SP - 192a EP - 192a ER - TY - JOUR T1 - Electrostatic Force Driven Molecular Dynamics Simulations AU - Peng, Y. AU - Koirala, M. AU - Alexov, E. JO - Biophysical Journal PY - 2019 PB - Elsevier VL - 116 IS - 3 SP - 290a EP - 290a ER - TY - JOUR T1 - A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry AU - Chakravorty, A. AU - Gallicchio, E. AU - Alexov, E. JO - Journal of computational chemistry PY - 2019 PB - John Wiley \& Sons, Inc. Hoboken, USA VL - 40 IS - 12 SP - 1290 EP - 1304 ER - TY - JOUR T1 - Structural perspective on revealing and altering molecular functions of genetic variants linked with diseases AU - Peng, Y. AU - Alexov, E. AU - Basu, S. JO - International journal of molecular sciences PY - 2019 PB - Multidisciplinary Digital Publishing Institute VL - 20 IS - 3 SP - 548 EP - 548 ER - TY - JOUR T1 - Structural Perspective on Revealing and Altering Molecular Mechanisms of Genetic Variants Linked with Diseases AU - Peng, Y. AU - Alexov, E. AU - Basu, S. PY - 2018 ER - TY - CHAP T1 - Modeling Tubulin E-Hooks Interactions with Dynein Microtubule Binding Domain AU - Tajielyato, N. AU - Alper, J. AU - Alexov, E. TI - PROTEIN SCIENCE PY - 2018 VL - 27 SP - 198 EP - 198 ER - TY - JOUR T1 - DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate AU - Pahari, S. AU - Sun, L. AU - Basu, S. AU - Alexov, E. JO - Proteins: Structure, Function, and Bioinformatics PY - 2018 PB - John Wiley \& Sons, Inc. Hoboken, USA VL - 86 IS - 12 SP - 1277 EP - 1283 ER - TY - JOUR T1 - E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein AU - Tajielyato, N. AU - Li, L. AU - Peng, Y. AU - Alper, J. AU - Alexov, E. JO - Scientific reports PY - 2018 PB - Nature Publishing Group VL - 8 IS - 1 SP - 1 EP - 10 ER - TY - JOUR T1 - Gaussian-based smooth dielectric function: a surface-free approach for modeling macromolecular binding in solvents AU - Chakravorty, A. AU - Jia, Z. AU - Peng, Y. AU - Tajielyato, N. AU - Wang, L. AU - Alexov, E. JO - Frontiers in molecular biosciences PY - 2018 PB - Frontiers VL - 5 SP - 25 EP - 25 ER - TY - JOUR T1 - The capricious electrostatic force: Revealing the signaling pathway in integrin $\alpha$ 2-I domain AU - Jia, Z. AU - Li, L. AU - Peng, Y. AU - Ding, F. AU - Alexov, E. JO - Journal of Theoretical and Computational Chemistry PY - 2018 PB - World Scientific Publishing Company VL - 17 IS - 3 SP - 1840001 EP - 1840001 ER - TY - JOUR T1 - Single Molecule Study of Long-Range Electrostatic Binding Affinity of Cytoplasmic Dynein's Microtubule Binding Domain AU - Godar, S. C. AU - Lovelace, H. AU - Eller, J. AU - Spencer, M. AU - Li, L. AU - Hamilton, G. AU - Sanabria, H. AU - Alexov, E. AU - Alper, J. JO - Biophysical Journal PY - 2018 PB - Elsevier VL - 114 IS - 3 SP - 512a EP - 512a ER - TY - JOUR T1 - Key apoptotic genes APAF1 and CASP9 implicated in recurrent folate-resistant neural tube defects AU - Spellicy, C. J. AU - Norris, J. AU - Bend, R. AU - Bupp, C. AU - Mester, P. AU - Reynolds, T. AU - Dean, J. AU - Peng, Y. AU - Alexov, E. AU - Schwartz, C. E. AU - others, JO - European Journal of Human Genetics PY - 2018 PB - Nature Publishing Group VL - 26 IS - 3 SP - 420 EP - 427 ER - TY - JOUR T1 - Reproducing the ensemble average polar solvation energy of a protein from a single structure: gaussian-based smooth dielectric function for macromolecular modeling AU - Chakravorty, A. AU - Jia, Z. AU - Li, L. AU - Zhao, S. AU - Alexov, E. JO - Journal of chemical theory and computation PY - 2018 PB - American Chemical Society VL - 14 IS - 2 SP - 1020 EP - 1032 ER - TY - JOUR T1 - Computational investigation of the missense mutations in DHCR7 gene associated with Smith-Lemli-Opitz syndrome AU - Peng, Y. AU - Myers, R. AU - Zhang, W. AU - Alexov, E. JO - International journal of molecular sciences PY - 2018 PB - Multidisciplinary Digital Publishing Institute VL - 19 IS - 1 SP - 141 EP - 141 ER - TY - JOUR T1 - Predicting protein--DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver AU - Peng, Y. AU - Sun, L. AU - Jia, Z. AU - Li, L. AU - Alexov, E. JO - Bioinformatics PY - 2018 PB - Oxford University Press VL - 34 IS - 5 SP - 779 EP - 786 ER - TY - CHAP T1 - Simulation study of integrin alpha-2 I domain activation AU - Jia, Z. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2017 VL - 254 ER - TY - CHAP T1 - Predicting binding free energy change caused by missense mutations in protein-DNA interactions using modified MM/PBSA method AU - Peng, Y. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2017 VL - 254 ER - TY - JOUR T1 - Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations AU - Li, L. AU - Jia, Z. AU - Peng, Y. AU - Godar, S. AU - Getov, I. AU - Teng, S. AU - Alper, J. AU - Alexov, E. JO - Scientific reports PY - 2017 PB - Nature Publishing Group VL - 7 IS - 1 SP - 1 EP - 12 ER - TY - JOUR T1 - Protein Conformational Disease: Visit the Facts at a Glance AU - Peng, Y. AU - Alexov, E. JO - eLS PY - 2017 PB - American Cancer Society SP - 1 EP - 7 ER - TY - JOUR T1 - DelPhiForce web server: electrostatic forces and energy calculations and visualization AU - Li, L. AU - Jia, Z. AU - Peng, Y. AU - Chakravorty, A. AU - Sun, L. AU - Alexov, E. JO - Bioinformatics PY - 2017 PB - Oxford University Press VL - 33 IS - 22 SP - 3661 EP - 3663 ER - TY - PAT T1 - Treating ion distribution with G aussian-based smooth dielectric function in DelPhi AU - Jia, Z. AU - Li, L. AU - Chakravorty, A. AU - Alexov, E. PY - 2017 ER - TY - JOUR T1 - Cytoskeletal-like Filaments of Ca2+-Calmodulin-Dependent Protein Kinase II Are Formed in a Regulated and Zn2+-Dependent Manner AU - Hoffman, L. AU - Li, L. AU - Alexov, E. AU - Sanabria, H. AU - Waxham, M. N. JO - Biochemistry PY - 2017 PB - American Chemical Society VL - 56 IS - 15 SP - 2149 EP - 2160 ER - TY - JOUR T1 - A new DelPhi feature for modeling electrostatic potential around proteins: Role of bound ions and implications for zeta-potential AU - Chakravorty, A. AU - Jia, Z. AU - Li, L. AU - Alexov, E. JO - Langmuir PY - 2017 PB - American Chemical Society VL - 33 IS - 9 SP - 2283 EP - 2295 ER - TY - JOUR T1 - Calcium Calmodulin Regulates Zinc Mediated Changes in the Structure, Self-Association, and Activity of CaMKII AU - Hoffman, L. AU - Li, L. AU - Alexov, E. AU - Waxham, M. N. AU - Sanabria, H. JO - Biophysical Journal PY - 2017 PB - Elsevier VL - 112 IS - 3 SP - 444a EP - 445a ER - TY - JOUR T1 - Multi-Scale Investigation on the Mechanisms of Dyneins’ Motion on Microtubule AU - Li, L. AU - Alper, J. AU - Alexov, E. JO - Biophysical Journal PY - 2017 PB - Elsevier VL - 112 IS - 3 SP - 261a EP - 261a ER - TY - JOUR T1 - DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding AU - Li, L. AU - Chakravorty, A. AU - Alexov, E. JO - Journal of computational chemistry PY - 2017 VL - 38 IS - 9 SP - 584 EP - 593 ER - TY - JOUR T1 - Computational investigation of proton transfer, p K a shifts and p H-optimum of protein--DNA and protein--RNA complexes AU - Peng, Y. AU - Alexov, E. JO - Proteins: Structure, Function, and Bioinformatics PY - 2017 VL - 85 IS - 2 SP - 282 EP - 295 ER - TY - CHAP T1 - Parallelization schemes for solving Poisson-Boltzmann equation via finite-difference method: Implementations in DelPhi and applications AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2016 VL - 252 ER - TY - JOUR T1 - Dielectric Properties of Biological Macromolecules and Biomolecule--Water Interfaces AU - Campbell, B. AU - Li, L. AU - Alexov, E. JO - Encyclopedia of Biocolloid and Biointerface Science 2V Set PY - 2016 PB - John Wiley \& Sons, Inc. Hoboken, NJ, USA SP - 380 EP - 390 ER - TY - JOUR T1 - Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model AU - Peng, Y. AU - Alexov, E. JO - Proteins: Structure, Function, and Bioinformatics PY - 2016 VL - 84 IS - 12 SP - 1797 EP - 1809 ER - TY - JOUR T1 - Electrostatic component of binding energy: interpreting predictions from poisson--boltzmann equation and modeling protocols AU - Chakavorty, A. AU - Li, L. AU - Alexov, E. JO - Journal of computational chemistry PY - 2016 VL - 37 IS - 28 SP - 2495 EP - 2507 ER - TY - JOUR T1 - Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions AU - Li, L. AU - Alper, J. AU - Alexov, E. JO - Scientific reports PY - 2016 PB - Nature Publishing Group VL - 6 IS - 1 SP - 1 EP - 12 ER - TY - JOUR T1 - Binding analysis of methyl-CpG binding domain of MeCP2 and Rett syndrome mutations AU - Yang, Y. AU - Kucukkal, T. G. AU - Li, J. AU - Alexov, E. AU - Cao, W. JO - ACS chemical biology PY - 2016 PB - American Chemical Society VL - 11 IS - 10 SP - 2706 EP - 2715 ER - TY - JOUR T1 - SAAMBE: webserver to predict the charge of binding free energy caused by amino acids mutations AU - Petukh, M. AU - Dai, L. AU - Alexov, E. JO - International journal of molecular sciences PY - 2016 PB - Multidisciplinary Digital Publishing Institute VL - 17 IS - 4 SP - 547 EP - 547 ER - TY - JOUR T1 - Revealing the effects of missense mutations causing Snyder-Robinson syndrome on the stability and dimerization of spermine synthase AU - Peng, Y. AU - Norris, J. AU - Schwartz, C. AU - Alexov, E. JO - International journal of molecular sciences PY - 2016 PB - Multidisciplinary Digital Publishing Institute VL - 17 IS - 1 SP - 77 EP - 77 ER - TY - JOUR T1 - SAAFEC: predicting the effect of single point mutations on protein folding free energy using a knowledge-modified MM/PBSA approach AU - Getov, I. AU - Petukh, M. AU - Alexov, E. JO - International journal of molecular sciences PY - 2016 PB - Multidisciplinary Digital Publishing Institute VL - 17 IS - 4 SP - 512 EP - 512 ER - TY - JOUR T1 - Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules AU - Li, L. AU - Alper, J. AU - Alexov, E. JO - Scientific reports PY - 2016 PB - Nature Publishing Group VL - 6 IS - 1 SP - 1 EP - 12 ER - TY - JOUR T1 - DelPhiPKa web server: predicting p K a of proteins, RNAs and DNAs AU - Wang, L. AU - Zhang, M. AU - Alexov, E. JO - Bioinformatics PY - 2016 PB - Oxford University Press VL - 32 IS - 4 SP - 614 EP - 615 ER - TY - JOUR T1 - Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding AU - Peng, Y. AU - Alexov, E. JO - Proteins: Structure, Function, and Bioinformatics PY - 2016 VL - 84 IS - 2 SP - 232 EP - 239 ER - TY - CHAP T1 - Predicting folding free energy changes caused by single point mutations via combined usage of MM-PBSA method and biophysical characteristics AU - Getov, I. AU - Petukh, M. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2015 VL - 250 ER - TY - JOUR T1 - Navigating through genomics data to deliver testable predictions AU - Alexov, E. JO - Human Mutation PY - 2015 VL - 36 IS - 2 SP - v EP - v ER - TY - JOUR T1 - SAMBE: The New Webserver for Predicting the Effect of nssNP on the Protein-Protein Binding Free Energy AU - Petukh, M. AU - Morrison, J. AU - Li, M. AU - Panchenko, A. AU - Alexov, E. JO - Biophysical Journal PY - 2015 PB - Elsevier VL - 108 IS - 2 SP - 157a EP - 158a ER - TY - JOUR T1 - Statistical investigation of surface bound ions and further development of BION server to include p H and salt dependence AU - Petukh, M. AU - Zhang, M. AU - Alexov, E. JO - Journal of computational chemistry PY - 2015 VL - 36 IS - 32 SP - 2381 EP - 2393 ER - TY - JOUR T1 - Structural, dynamical, and energetical consequences of Rett syndrome mutation R133C in MeCP2 AU - Kucukkal, T. G. AU - Alexov, E. JO - Computational and mathematical methods in medicine PY - 2015 PB - Hindawi VL - 2015 ER - TY - JOUR T1 - Impact of rett syndrome mutations on MeCP2 MBD stability AU - Kucukkal, T. G. AU - Yang, Y. AU - Uvarov, O. AU - Cao, W. AU - Alexov, E. JO - Biochemistry PY - 2015 PB - American Chemical Society VL - 54 IS - 41 SP - 6357 EP - 6368 ER - TY - JOUR T1 - Mutations in the KDM5C ARID domain and their plausible association with syndromic Claes-Jensen-Type disease AU - Peng, Y. AU - Suryadi, J. AU - Yang, Y. AU - Kucukkal, T. G. AU - Cao, W. AU - Alexov, E. JO - International journal of molecular sciences PY - 2015 PB - Multidisciplinary Digital Publishing Institute VL - 16 IS - 11 SP - 27270 EP - 27287 ER - TY - JOUR T1 - On the energy components governing molecular recognition in the framework of continuum approaches AU - Li, L. AU - Wang, L. AU - Alexov, E. JO - Frontiers in molecular biosciences PY - 2015 PB - Frontiers VL - 2 SP - 5 EP - 5 ER - TY - JOUR T1 - Predicting binding free energy change caused by point mutations with knowledge-modified MM/PBSA method AU - Petukh, M. AU - Li, M. AU - Alexov, E. JO - PLoS computational biology PY - 2015 PB - Public Library of Science San Francisco, CA USA VL - 11 IS - 7 SP - e1004276 EP - e1004276 ER - TY - JOUR T1 - pKa predictions for proteins, RNA s, and DNA s with the Gaussian dielectric function using DelPhi pKa AU - Wang, L. AU - Li, L. AU - Alexov, E. JO - Proteins: Structure, Function, and Bioinformatics PY - 2015 VL - 83 IS - 12 SP - 2186 EP - 2197 ER - TY - JOUR T1 - On human disease-causing amino acid variants: Statistical study of sequence and structural patterns AU - Petukh, M. AU - Kucukkal, T. G. AU - Alexov, E. JO - Human mutation PY - 2015 VL - 36 IS - 5 SP - 524 EP - 534 ER - TY - JOUR T1 - Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins AU - Kucukkal, T. G. AU - Petukh, M. AU - Li, L. AU - Alexov, E. JO - Current opinion in structural biology PY - 2015 PB - Elsevier Current Trends VL - 32 SP - 18 EP - 24 ER - TY - PAT T1 - Electrostatics and polarization effects in biophysical chemistry: in silico and in vitro AU - Alexov, E. AU - Luo, R. PY - 2014 PB - WORLD SCIENTIFIC PUBL CO PTE LTD 5 TOH TUCK LINK, SINGAPORE 596224, SINGAPORE ER - TY - JOUR T1 - Rational Design of Small-Molecule Stabilizers of Spermine Synthase Dimer by Virtual AU - Zhang, Z. AU - Martiny, V. AU - Lagorce, D. AU - Ikeguchi, Y. AU - Alexov, E. AU - others, PY - 2014 ER - TY - CHAP T1 - Modeling ensemble-averaged electrostatics with smooth Gaussian-based dielectric function AU - Li, L. AU - Smith, N. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2014 VL - 248 ER - TY - JOUR T1 - Molecular mechanisms underlying pathogenic missense mutations AU - Wu, B. AU - Eggert, J. AU - Alexov, E. JO - eLS PY - 2014 PB - American Cancer Society ER - TY - JOUR T1 - On the electrostatic properties of homodimeric proteins AU - Campbell, B. AU - Petukh, M. AU - Alexov, E. AU - Li, C. JO - Journal of Theoretical and Computational Chemistry PY - 2014 PB - World Scientific Publishing Company VL - 13 IS - 3 SP - 1440007 EP - 1440007 ER - TY - JOUR T1 - Ion binding to biological macromolecules AU - Petukh, M. AU - Alexov, E. JO - Asian journal of physics: an international quarterly research journal PY - 2014 PB - NIH Public Access VL - 23 IS - 5 SP - 735 EP - 735 ER - TY - JOUR T1 - Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity AU - Nedumpully-Govindan, P. AU - Li, L. AU - Alexov, E. G. AU - Blenner, M. A. AU - Ding, F. JO - Bioinformatics PY - 2014 PB - Oxford University Press VL - 30 IS - 16 SP - 2302 EP - 2309 ER - TY - JOUR T1 - Advances in human biology: combining genetics and molecular biophysics to pave the way for personalized diagnostics and medicine AU - Alexov, E. JO - Advances in Biology PY - 2014 PB - Hindawi VL - 2014 ER - TY - JOUR T1 - Chronic beryllium disease: revealing the role of beryllium ion and small peptides binding to HLA-DP2 AU - Petukh, M. AU - Wu, B. AU - Stefl, S. AU - Smith, N. AU - Hyde-Volpe, D. AU - Wang, L. AU - Alexov, E. JO - PLoS One PY - 2014 PB - Public Library of Science VL - 9 IS - 11 SP - e111604 EP - e111604 ER - TY - JOUR T1 - ProBLM web server: protein and membrane placement and orientation package AU - Kimmett, T. AU - Smith, N. AU - Witham, S. AU - Petukh, M. AU - Sarkar, S. AU - Alexov, E. JO - Computational and mathematical methods in medicine PY - 2014 PB - Hindawi VL - 2014 ER - TY - JOUR T1 - Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: the MEMPOT algorithm implemented in DelPhi AU - Dias, R. P. AU - Li, L. AU - Soares, T. A. AU - Alexov, E. JO - Journal of computational chemistry PY - 2014 VL - 35 IS - 19 SP - 1418 EP - 1429 ER - TY - JOUR T1 - On the modeling of polar component of solvation energy using smooth Gaussian-based dielectric function AU - Li, L. AU - Li, C. AU - Alexov, E. JO - Journal of Theoretical and Computational Chemistry PY - 2014 PB - World Scientific Publishing Company VL - 13 IS - 3 SP - 1440002 EP - 1440002 ER - TY - JOUR T1 - Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach AU - Zhang, Z. AU - Martiny, V. AU - Lagorce, D. AU - Ikeguchi, Y. AU - Alexov, E. AU - Miteva, M. A. JO - PLoS One PY - 2014 PB - Public Library of Science VL - 9 IS - 10 SP - e110884 EP - e110884 ER - TY - JOUR T1 - 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 AU - Dolzhanskaya, N. AU - Gonzalez, M. A. AU - Sperziani, F. AU - Stefl, S. AU - Messing, J. AU - Wen, G. Y. AU - Alexov, E. AU - Zuchner, S. AU - Velinov, M. JO - Journal of Alzheimer's Disease PY - 2014 PB - IOS Press VL - 39 IS - 1 SP - 23 EP - 27 ER - TY - JOUR T1 - Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics AU - Kucukkal, T. G. AU - Yang, Y. AU - Chapman, S. C. AU - Cao, W. AU - Alexov, E. JO - International journal of molecular sciences PY - 2014 PB - Multidisciplinary Digital Publishing Institute VL - 15 IS - 6 SP - 9670 EP - 9717 ER - TY - JOUR T1 - Predicting the impact of missense mutations on protein--protein binding affinity AU - Li, M. AU - Petukh, M. AU - Alexov, E. AU - Panchenko, A. R. JO - Journal of chemical theory and computation PY - 2014 PB - American Chemical Society VL - 10 IS - 4 SP - 1770 EP - 1780 ER - TY - CHAP T1 - Electrostatics and polarization effects in biophysical chemistry: In silico, in vitro, and in vivo AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2013 VL - 246 ER - TY - CHAP T1 - Electrostatics plays significant role in changes of the protein-protein affinity due to missense mutations AU - Petukh, M. AU - Panchenko, A. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2013 VL - 246 ER - TY - CHAP T1 - Smooth dielectric function for modeling electrostatics in biological macromolecules AU - Li, L. AU - Li, C. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2013 VL - 246 ER - TY - JOUR T1 - Multi-Level and Interleaved Poisson-Boltzmann (MLIPB) Method for Parallel Computing of the Electrostatics and its Application in Delphi AU - Li, C. AU - Petukh, M. AU - Li, L. AU - Alexov, E. JO - Biophysical Journal PY - 2013 PB - Elsevier VL - 104 IS - 2 SP - 507a EP - 507a ER - TY - CHAP T1 - Characterizing a missense mutation in O-GlcNAc transferase that segregates with disease in a family with X-linked Intellectual Disability AU - Vaidyanathan, K. AU - Niranjan, T. AU - May, M. AU - Rose, R. AU - Teo, C. F. AU - Prabakaran, S. AU - Bridger, R. AU - Alexov, E. AU - Wang, T. AU - Schwartz, C. AU - others, TI - GLYCOBIOLOGY PY - 2013 VL - 23 IS - 11 SP - 1334 EP - 1335 ER - TY - CHAP T1 - Snyder-Robinson Syndrome: Rescuing the Disease-Causing Effect of G56S mutant by Small Molecule Binding AU - Zhang, Z. AU - Martiny, V. AU - Lagorce, D. AU - Alexov, E. AU - Miteva, M. AU - others, TI - APS March Meeting Abstracts PY - 2013 VL - 2013 SP - G45 EP - 005 ER - TY - JOUR T1 - Modeling Proteins and Small Molecules with Inhomogeneous Dielectric Function: Implementation in Delphi AU - Li, L. AU - Li, C. AU - Alexov, E. JO - Biophysical Journal PY - 2013 PB - Elsevier VL - 104 IS - 2 SP - 35a EP - 35a ER - TY - JOUR T1 - Preface: Special Issue on Modeling Electrostatics in Molecular Biology (MEMB) AU - Alexov, E. AU - Wei, G.-W. JO - Communications in Computational Physics PY - 2013 PB - Cambridge University Press VL - 13 IS - 1 SP - i EP - v ER - TY - JOUR T1 - Enhancing Human Spermine Synthase Activity by Site Directed Mutations AU - Zhang, Z. AU - Pegg, A. AU - Ikeguchi, Y. AU - Alexov, E. JO - Biophysical Journal PY - 2013 PB - Elsevier VL - 104 IS - 2 SP - 380a EP - 380a ER - TY - JOUR T1 - Predicting non-specifically bound ions: Application to BION webserver and beryllium disease AU - Petukh, M. AU - Li, C. AU - Alexov, E. JO - Biophysical Journal PY - 2013 PB - Elsevier VL - 104 IS - 2 SP - 506a EP - 506a ER - TY - JOUR T1 - BION web server: predicting non-specifically bound surface ions AU - Petukh, M. AU - Kimmet, T. AU - Alexov, E. JO - Bioinformatics PY - 2013 PB - Oxford University Press VL - 29 IS - 6 SP - 805 EP - 806 ER - TY - JOUR T1 - Understanding molecular effects of naturally occurring genetic differences. AU - Alexov, E. AU - Sternberg, M. JO - Journal of molecular biology PY - 2013 VL - 425 IS - 21 SP - 3911 EP - 3913 ER - TY - JOUR T1 - Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi AU - Li, C. AU - Petukh, M. AU - Li, L. AU - Alexov, E. JO - Journal of computational chemistry PY - 2013 PB - Wiley Online Library VL - 34 IS - 22 SP - 1949 EP - 1960 ER - TY - JOUR T1 - In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor AU - Wang, L. AU - Witham, S. AU - Zhang, Z. AU - Li, L. AU - Hodsdon, M. E. AU - Alexov, E. JO - Communications in computational physics PY - 2013 PB - NIH Public Access VL - 13 IS - 1 SP - 207 EP - 207 ER - TY - JOUR T1 - A rational free energy-based approach to understanding and targeting disease-causing missense mutations AU - Zhang, Z. AU - Witham, S. AU - Petukh, M. AU - Moroy, G. AU - Miteva, M. AU - Ikeguchi, Y. AU - Alexov, E. JO - Journal of the American Medical Informatics Association PY - 2013 PB - BMJ Publishing Group BMA House, Tavistock Square, London, WC1H 9JR VL - 20 IS - 4 SP - 643 EP - 651 ER - TY - JOUR T1 - Enhancing human spermine synthase activity by engineered mutations AU - Zhang, Z. AU - Zheng, Y. AU - Petukh, M. AU - Pegg, A. AU - Ikeguchi, Y. AU - Alexov, E. JO - PLoS Comput Biol PY - 2013 PB - Public Library of Science VL - 9 IS - 2 SP - e1002924 EP - e1002924 ER - TY - JOUR T1 - DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes AU - Sarkar, S. AU - Witham, S. AU - Zhang, J. AU - Zhenirovskyy, M. AU - Rocchia, W. AU - Alexov, E. JO - Communications in computational physics PY - 2013 PB - NIH Public Access VL - 13 IS - 1 SP - 269 EP - 269 ER - TY - JOUR T1 - Using DelPhi capabilities to mimic protein’s conformational reorganization with amino acid specific dielectric constants AU - Wang, L. AU - Zhang, Z. AU - Rocchia, W. AU - Alexov, E. JO - Communications in computational physics PY - 2013 PB - NIH Public Access VL - 13 IS - 1 SP - 13 EP - 13 ER - TY - JOUR T1 - Progress in developing Poisson-Boltzmann equation solvers AU - Li, C. AU - Li, L. AU - Petukh, M. AU - Alexov, E. JO - Computational and Mathematical Biophysics PY - 2013 PB - De Gruyter VL - 1 IS - 1 SP - 42 EP - 62 ER - TY - JOUR T1 - A Y328C missense mutation in spermine synthase causes a mild form of Snyder--Robinson syndrome AU - Zhang, Z. AU - Norris, J. AU - Kalscheuer, V. AU - Wood, T. AU - Wang, L. AU - Schwartz, C. AU - Alexov, E. AU - Esch, H. V. JO - Human molecular genetics PY - 2013 PB - Oxford University Press VL - 22 IS - 18 SP - 3789 EP - 3797 ER - TY - JOUR T1 - The role of protonation states in ligand-receptor recognition and binding AU - Petukh, M. AU - Stefl, S. AU - Alexov, E. JO - Current pharmaceutical design PY - 2013 PB - Bentham Science Publishers VL - 19 IS - 23 SP - 4182 EP - 4190 ER - TY - JOUR T1 - Between algorithm and model: different molecular surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution AU - Decherchi, S. AU - Colmenares, J. AU - Catalano, C. E. AU - Spagnuolo, M. AU - Alexov, E. AU - Rocchia, W. JO - Communications in computational physics PY - 2013 PB - NIH Public Access VL - 13 SP - 61 EP - 61 ER - TY - JOUR T1 - Protonation and pK changes in protein-ligand binding AU - Onufriev, A. V. AU - Alexov, E. JO - Quarterly reviews of biophysics PY - 2013 PB - NIH Public Access VL - 46 IS - 2 SP - 181 EP - 181 ER - TY - JOUR T1 - Cancer missense mutations alter binding properties of proteins and their interaction networks AU - Nishi, H. AU - Tyagi, M. AU - Teng, S. AU - Shoemaker, B. A. AU - Hashimoto, K. AU - Alexov, E. AU - Wuchty, S. AU - Panchenko, A. R. JO - PloS one PY - 2013 PB - Public Library of Science VL - 8 IS - 6 SP - e66273 EP - e66273 ER - TY - JOUR T1 - Molecular mechanisms of disease-causing missense mutations AU - Stefl, S. AU - Nishi, H. AU - Petukh, M. AU - Panchenko, A. R. AU - Alexov, E. JO - Journal of molecular biology PY - 2013 PB - Academic Press VL - 425 IS - 21 SP - 3919 EP - 3936 ER - TY - JOUR T1 - On the dielectric “constant” of proteins: smooth dielectric function for macromolecular modeling and its implementation in DelPhi AU - Li, L. AU - Li, C. AU - Zhang, Z. AU - Alexov, E. JO - Journal of chemical theory and computation PY - 2013 PB - American Chemical Society VL - 9 IS - 4 SP - 2126 EP - 2136 ER - TY - CHAP T1 - Parallelized DelPhi: A multiprocessor Poisson-Boltzmann solver to calculate electrostatic energies of biological macromolecules AU - Li, C. AU - Li, L. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2012 VL - 244 ER - TY - JOUR T1 - CALCULATION OF ELECTROSTATIC FORCES AU - GUNNER, M. R. AU - ALEXOV, E. JO - Molecular Modeling and Dynamics of Bioinorganic Systems PY - 2012 PB - Springer Science \& Business Media VL - 41 SP - 361 EP - 361 ER - TY - JOUR T1 - New Parallelized DelPhi: Fast and Efficient Poisson-Boltzmann Solver to Calculate Electrostatics of Large Supramolecular Structures AU - Li, C. AU - Zhenirovskyy, M. AU - Li, L. AU - Alexov, E. JO - Biophysical Journal PY - 2012 PB - Elsevier VL - 102 IS - 3 SP - 270a EP - 270a ER - TY - JOUR T1 - Modeling CLIC2-RyR Interactions and the Effect of Disease Causing Mutation AU - Witham, S. AU - Alexov, E. JO - Biophysical Journal PY - 2012 PB - Elsevier VL - 102 IS - 3 SP - 456a EP - 456a ER - TY - CHAP T1 - Effect of non-uniform protein dielectric constant on the electrostatic energy calculations AU - Li, L. AU - Wang, L. AU - Li, C. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2012 VL - 244 ER - TY - JOUR T1 - Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling AU - Smith, N. AU - Campbell, B. AU - Li, L. AU - Li, C. AU - Alexov, E. JO - BMC structural biology PY - 2012 PB - BioMed Central VL - 12 IS - 1 SP - 1 EP - 10 ER - TY - JOUR T1 - Predicting nonspecific ion binding using DelPhi AU - Petukh, M. AU - Zhenirovskyy, M. AU - Li, C. AU - Li, L. AU - Wang, L. AU - Alexov, E. JO - Biophysical journal PY - 2012 PB - Elsevier VL - 102 IS - 12 SP - 2885 EP - 2893 ER - TY - JOUR T1 - Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi AU - Li, C. AU - Li, L. AU - Zhang, J. AU - Alexov, E. JO - Journal of computational chemistry PY - 2012 PB - Wiley Online Library VL - 33 IS - 24 SP - 1960 EP - 1966 ER - TY - JOUR T1 - DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol AU - Smith, N. AU - Witham, S. AU - Sarkar, S. AU - Zhang, J. AU - Li, L. AU - Li, C. AU - Alexov, E. JO - Bioinformatics PY - 2012 PB - Oxford University Press VL - 28 IS - 12 SP - 1655 EP - 1657 ER - TY - JOUR T1 - Predicting folding free energy changes upon single point mutations AU - Zhang, Z. AU - Wang, L. AU - Gao, Y. AU - Zhang, J. AU - Zhenirovskyy, M. AU - Alexov, E. JO - Bioinformatics PY - 2012 PB - Oxford University Press VL - 28 IS - 5 SP - 664 EP - 671 ER - TY - JOUR T1 - An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity AU - Takano, K. AU - Liu, D. AU - Tarpey, P. AU - Gallant, E. AU - Lam, A. AU - Witham, S. AU - Alexov, E. AU - Chaubey, A. AU - Stevenson, R. E. AU - Schwartz, C. E. AU - others, JO - Human molecular genetics PY - 2012 PB - Oxford University Press VL - 21 IS - 20 SP - 4497 EP - 4507 ER - TY - JOUR T1 - Analyzing effects of naturally occurring missense mutations AU - Zhang, Z. AU - Miteva, M. A. AU - Wang, L. AU - Alexov, E. JO - Computational and mathematical methods in medicine PY - 2012 PB - Hindawi VL - 2012 ER - TY - JOUR T1 - DelPhi: a comprehensive suite for DelPhi software and associated resources AU - Li, L. AU - Li, C. AU - Sarkar, S. AU - Zhang, J. AU - Witham, S. AU - Zhang, Z. AU - Wang, L. AU - Smith, N. AU - Petukh, M. AU - Alexov, E. JO - BMC biophysics PY - 2012 PB - BioMed Central VL - 5 IS - 1 SP - 1 EP - 11 ER - TY - JOUR T1 - In Silico and In Vitro Investigations of the Mutability of Disease-Causing Missense Mutation Sites in AU - Zhang, Z. AU - Norris, J. AU - Schwartz, C. AU - Alexov, E. PY - 2011 ER - TY - CHAP T1 - In silico investigation of molecular effects caused by missense mutations in creatine transporter protein AU - Zhang, Z. AU - Schwatz, C. AU - Alexov, E. TI - APS March Meeting Abstracts PY - 2011 VL - 2011 SP - T39 EP - 002 ER - TY - CHAP T1 - Using DelPhi capabilities to mimic conformational reorganization with amino acid specific dielectric constants AU - Wang, L. AU - Sarhar, S. AU - Rocchia, W. AU - Alexov, E. TI - APS March Meeting Abstracts PY - 2011 VL - 2011 SP - S1 EP - 156 ER - TY - JOUR T1 - In Silico Investigation of Mutability of Spermine Synthase AU - Zhang, Z. AU - Schwartz, C. AU - Alexov, E. JO - Biophysical Journal PY - 2011 PB - Elsevier VL - 100 IS - 3 SP - 321a EP - 321a ER - TY - JOUR T1 - $\backslash$textit $\{$In silico$\}$ investigation of molecular effects caused by missense mutations in creatine transporter protein AU - Zhang, Z. AU - Schwatz, C. AU - Alexov, E. JO - Bulletin of the American Physical Society PY - 2011 PB - American Physical Society VL - 56 ER - TY - JOUR T1 - In Silico Investigation of a Missense Mutation in CLIC2 Associated with Intellectual Disability AU - Witham, S. AU - Takano, K. AU - Schwartz, C. AU - Alexov, E. JO - Biophysical Journal PY - 2011 PB - Elsevier VL - 100 IS - 3 SP - 611a EP - 611a ER - TY - CHAP T1 - DelPhi webserver: Comprehensive suite for electrostatic calculations of biological macromolecules and their complexes AU - Witham, S. AU - Boylen, B. AU - Owesen, B. AU - Rocchia, W. AU - Alexov, E. TI - APS March Meeting Abstracts PY - 2011 VL - 2011 SP - S1 EP - 155 ER - TY - JOUR T1 - Developing hybrid approaches to predict pKa values of ionizable groups AU - Witham, S. AU - Talley, K. AU - Wang, L. AU - Zhang, Z. AU - Sarkar, S. AU - Gao, D. AU - Yang, W. AU - Alexov, E. JO - Proteins: Structure, Function, and Bioinformatics PY - 2011 PB - Wiley Subscription Services, Inc., A Wiley Company Hoboken VL - 79 IS - 12 SP - 3389 EP - 3399 ER - TY - JOUR T1 - A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics AU - Witham, S. AU - Takano, K. AU - Schwartz, C. AU - Alexov, E. JO - Proteins: Structure, Function, and Bioinformatics PY - 2011 PB - Wiley Subscription Services, Inc., A Wiley Company Hoboken VL - 79 IS - 8 SP - 2444 EP - 2454 ER - TY - JOUR T1 - In silico modeling of pH-optimum of protein--protein binding AU - Mitra, R. C. AU - Zhang, Z. AU - Alexov, E. JO - Proteins: Structure, Function, and Bioinformatics PY - 2011 PB - Wiley Subscription Services, Inc., A Wiley Company Hoboken VL - 79 IS - 3 SP - 925 EP - 936 ER - TY - JOUR T1 - In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in spermine synthase AU - Zhang, Z. AU - Norris, J. AU - Schwartz, C. AU - Alexov, E. JO - PloS one PY - 2011 PB - Public Library of Science VL - 6 IS - 5 SP - e20373 EP - e20373 ER - TY - JOUR T1 - On the role of electrostatics in protein--protein interactions AU - Zhang, Z. AU - Witham, S. AU - Alexov, E. JO - Physical biology PY - 2011 PB - IOP Publishing VL - 8 IS - 3 SP - 035001 EP - 035001 ER - TY - JOUR T1 - Progress in the prediction of pKa values in proteins AU - Alexov, E. AU - Mehler, E. L. AU - Baker, N. AU - Baptista, A. M. AU - Huang, Y. AU - Milletti, F. AU - Nielsen, J. E. AU - Farrell, D. AU - Carstensen, T. AU - Olsson, M. H. AU - others, JO - Proteins: structure, function, and bioinformatics PY - 2011 PB - Wiley Subscription Services, Inc., A Wiley Company Hoboken VL - 79 IS - 12 SP - 3260 EP - 3275 ER - TY - JOUR T1 - From 2010 Abstracts Issue AU - Zhe, Z. AU - Shaolei, T. AU - Alexov, E. JO - Biophysical Journal PY - 2010 VL - 98 SP - 1096 EP - 1098 ER - TY - CHAP T1 - Structural and Energetic Basis of Molecular Recognition AU - Alexov, E. AU - Honig, B. TI - Handbook of Cell Signaling PY - 2010 PB - Academic Press SP - 11 EP - 13 ER - TY - JOUR T1 - PMCID: PMC2695060. AU - Pittman, A. AU - Saul, R. AU - Chaubey, A. AU - Alexov, E. AU - Tiemeyer, M. AU - Steet, R. AU - Schwartz, C. AU - B\'en\'eteau, M. AU - Ricci, J. AU - Desquiret-Dumas, V. AU - others, JO - Int Immunol PY - 2010 VL - 22 IS - 7 SP - 593 EP - 603 ER - TY - JOUR T1 - In Silico Investigation of the Molecular Effects Caused by Missense Mutations in Spermine Sythase Gene Associated with Human Mental Retardation AU - Zhe, Z. AU - Shaolei, T. AU - Alexov, E. JO - Biophysical Journal PY - 2010 PB - Elsevier VL - 98 IS - 3 SP - 571a EP - 571a ER - TY - JOUR T1 - Structural assessment of the effects of Amino Acid Substitutions on protein stability and protein? protein interaction AU - Teng, S. AU - Srivastava, A. K. AU - Schwartz, C. E. AU - Alexov, E. AU - Wang, L. JO - International journal of computational biology and drug design PY - 2010 PB - Inderscience Publishers VL - 3 IS - 4 SP - 334 EP - 349 ER - TY - JOUR T1 - On the pH-optimum of activity and stability of proteins AU - Talley, K. AU - Alexov, E. JO - Proteins: Structure, Function, and Bioinformatics PY - 2010 PB - Wiley Subscription Services, Inc., A Wiley Company Hoboken VL - 78 IS - 12 SP - 2699 EP - 2706 ER - TY - JOUR T1 - Computational analysis of missense mutations causing Snyder-Robinson syndrome AU - Zhang, Z. AU - Teng, S. AU - Wang, L. AU - Schwartz, C. E. AU - Alexov, E. JO - Human mutation PY - 2010 PB - Wiley Subscription Services, Inc., A Wiley Company Hoboken VL - 31 IS - 9 SP - 1043 EP - 1049 ER - TY - CHAP T1 - Modeling Ionization Events iduced by Protein Protein Binding AU - Mitra, R. AU - Shyam, R. AU - Alexov, E. TI - APS Southeastern Section Meeting Abstracts PY - 2009 VL - 76 SP - PC EP - 003 ER - TY - CHAP T1 - Multivariate Analysis of Conformational Changes Induced by Macromolecular Interactions AU - Mitra, I. AU - Alexov, E. TI - APS Southeastern Section Meeting Abstracts PY - 2009 VL - 76 SP - PC EP - 004 ER - TY - JOUR T1 - Modeling effects of human single nucleotide polymorphisms on protein-protein interactions.(vol 96, pg 2178, 2009) AU - Teng, S. AU - Madej, T. AU - Panchenko, A. AU - Alexov, E. JO - BIOPHYSICAL JOURNAL PY - 2009 PB - CELL PRESS 600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA VL - 96 IS - 11 SP - 4753 EP - 4753 ER - TY - CHAP T1 - Accessing the limits of ab initio docking methods AU - Shyam, R. AU - Alexov, E. TI - APS Southeastern Section Meeting Abstracts PY - 2009 VL - 76 SP - PC EP - 002 ER - TY - CHAP T1 - Computational Modeling of Molecular Effects of Mutations Causing Snyder-Robinson Syndrome AU - Zhang, Z. AU - Teng, S. AU - Alexov, E. TI - APS Southeastern Section Meeting Abstracts PY - 2009 VL - 76 SP - PC EP - 007 ER - TY - JOUR T1 - Modeling effects of human single nucleotide polymorphisms on protein-protein interactions AU - Teng, S. AU - Madej, T. AU - Panchenko, A. AU - Alexov, E. JO - Biophysical journal PY - 2009 PB - Elsevier VL - 96 IS - 6 SP - 2178 EP - 2188 ER - TY - JOUR T1 - Editorial [Protein-Protein Interactions Guest Editor: Emil Alexov] AU - Alexov, E. JO - Current pharmaceutical biotechnology PY - 2008 PB - Bentham Science Publishers VL - 9 IS - 2 SP - 55 EP - 56 ER - TY - JOUR T1 - Modeling salt dependence of protein-protein association: Linear vs non-linear Poisson-Boltzmann equation AU - Talley, K. AU - Kundrotas, P. AU - Alexov, E. JO - Commun Comput Phys PY - 2008 VL - 3 IS - 5 SP - 1071 EP - 1086 ER - TY - JOUR T1 - Calculating the protonation states of proteins and small molecules: Implications to ligand-receptor interactions AU - Mitra, R. AU - Shyam, R. AU - Mitra, I. AU - Miteva, M. A. AU - Alexov, E. JO - Current computer-aided drug design PY - 2008 PB - Bentham Science Publishers VL - 4 IS - 3 SP - 169 EP - 179 ER - TY - JOUR T1 - Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation AU - Kosloff, M. AU - Alexov, E. AU - Arshavsky, V. Y. AU - Honig, B. JO - Journal of Biological Chemistry PY - 2008 PB - Elsevier VL - 283 IS - 45 SP - 31197 EP - 31207 ER - TY - JOUR T1 - On the electrostatic component of protein-protein binding free energy AU - Talley, K. AU - Ng, C. AU - Shoppell, M. AU - Kundrotas, P. AU - Alexov, E. JO - PMC biophysics PY - 2008 PB - BioMed Central VL - 1 IS - 1 SP - 1 EP - 23 ER - TY - JOUR T1 - Homology-based modeling of 3D structures of protein--protein complexes using alignments of modified sequence profiles AU - Kundrotas, P. J. AU - Lensink, M. F. AU - Alexov, E. JO - International journal of biological macromolecules PY - 2008 PB - Elsevier VL - 43 IS - 2 SP - 198 EP - 208 ER - TY - JOUR T1 - Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions AU - Teng, S. AU - Michonova-Alexova, E. AU - Alexov, E. JO - Current pharmaceutical biotechnology PY - 2008 PB - Bentham Science Publishers VL - 9 IS - 2 SP - 123 EP - 133 ER - TY - CHAP T1 - Optimization of the electrostatic interactions in protein-protein complexes AU - Alexov, E. AU - Brock, K. AU - Kundrotas, P. TI - APS March Meeting Abstracts PY - 2007 SP - K1 EP - 021 ER - TY - CHAP T1 - Modeling protein-protein interactions with continuum electrostatics AU - Alexov, E. G. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2007 VL - 233 SP - 52 EP - 52 ER - TY - CHAP T1 - Utilizing Profile-to-Profile Alignments for Predicting Protein-Protein Interactions AU - Kundrotas, P. AU - Alexov, E. TI - APS March Meeting Abstracts PY - 2007 SP - K1 EP - 020 ER - TY - CHAP T1 - Predicting protein-protein interactions using non-gapped interacting residue segments AU - Kundrotas, P. AU - Alexov, E. TI - BIOPHYSICAL JOURNAL PY - 2007 SP - 367A EP - 368A ER - TY - JOUR T1 - BANMOKI: A searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families AU - Kundrotas, P. AU - Georgieva, P. AU - Shosheva, A. AU - Christova, P. AU - Alexov, E. JO - International journal of biological macromolecules PY - 2007 PB - Elsevier VL - 41 IS - 1 SP - 114 EP - 119 ER - TY - JOUR T1 - Protein Structure Analysis Online AU - Miteva, M. A. AU - Alexov, E. AU - Villoutreix, B. O. JO - Current protocols in protein science PY - 2007 VL - 50 IS - 1 SP - 2 EP - 13 ER - TY - JOUR T1 - Predicting interacting and interfacial residues using continuous sequence segments AU - Kundrotas, P. AU - Alexov, E. JO - International journal of biological macromolecules PY - 2007 PB - Elsevier VL - 41 IS - 5 SP - 615 EP - 623 ER - TY - JOUR T1 - Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families AU - Kundrotas, P. AU - Georgieva, P. AU - Shosheva, A. AU - Christova, P. AU - Alexov, E. JO - Journal of bioinformatics and computational biology PY - 2007 PB - World Scientific VL - 5 IS - 3 SP - 693 EP - 715 ER - TY - JOUR T1 - Electrostatic control of the overall shape of calmodulin: numerical calculations AU - Isvoran, A. AU - Craescu, C. AU - Alexov, E. JO - European Biophysics Journal PY - 2007 PB - Springer-Verlag VL - 36 IS - 3 SP - 225 EP - 237 ER - TY - JOUR T1 - Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase AU - Ofiteru, A. AU - Bucurenci, N. AU - Alexov, E. AU - Bertrand, T. AU - Briozzo, P. AU - Munier-Lehmann, H. AU - Gilles, A.-M. JO - The FEBS journal PY - 2007 PB - Blackwell Publishing Ltd Oxford, UK VL - 274 IS - 13 SP - 3363 EP - 3373 ER - TY - JOUR T1 - Optimization of electrostatic interactions in protein-protein complexes AU - Brock, K. AU - Talley, K. AU - Coley, K. AU - Kundrotas, P. AU - Alexov, E. JO - Biophysical journal PY - 2007 PB - Elsevier VL - 93 IS - 10 SP - 3340 EP - 3352 ER - TY - JOUR T1 - PROTCOM: searchable database of protein complexes enhanced with domain--domain structures AU - Kundrotas, P. J. AU - Alexov, E. JO - Nucleic Acids Research PY - 2007 PB - Oxford University Press VL - 35 IS - 1 SP - D575 EP - D579 ER - TY - JOUR T1 - Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies AU - Bertonati, C. AU - Honig, B. AU - Alexov, E. JO - Biophysical journal PY - 2007 PB - Elsevier VL - 92 IS - 6 SP - 1891 EP - 1899 ER - TY - JOUR T1 - Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides AU - Tang, C. L. AU - Alexov, E. AU - Pyle, A. M. AU - Honig, B. JO - Journal of molecular biology PY - 2007 PB - Academic Press VL - 366 IS - 5 SP - 1475 EP - 1496 ER - TY - CHAP T1 - Optimum pH for protein-protein complexes. AU - Kundrotas, P. AU - Alexov, E. TI - APS March Meeting Abstracts PY - 2006 SP - C1 EP - 121 ER - TY - CHAP T1 - Combining biophysical and bioinformatical approaches for predicting residue's contacts. AU - Alexov, E. AU - Allardice, A. AU - Kundrotas, P. TI - APS March Meeting Abstracts PY - 2006 SP - A26 EP - 014 ER - TY - CHAP T1 - Predicting 3D structures of transient protein-protein complexes AU - Kundrotas, P. AU - Alexov, E. TI - APS March Meeting Abstracts PY - 2006 SP - A26 EP - 007 ER - TY - JOUR T1 - Predicting 3D structures of transient protein--protein complexes by homology AU - Kundrotas, P. J. AU - Alexov, E. JO - Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics PY - 2006 PB - Elsevier VL - 1764 IS - 9 SP - 1498 EP - 1511 ER - TY - JOUR T1 - Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives AU - Kundrotas, P. J. AU - Alexov, E. G. JO - BMC bioinformatics PY - 2006 PB - BioMed Central VL - 7 IS - 1 SP - 1 EP - 9 ER - TY - JOUR T1 - Electrostatic properties of protein-protein complexes AU - Kundrotas, P. J. AU - Alexov, E. JO - Biophysical journal PY - 2006 PB - Elsevier VL - 91 IS - 5 SP - 1724 EP - 1736 ER - TY - JOUR T1 - 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 AU - Grey, M. J. AU - Tang, Y. AU - Alexov, E. AU - McKnight, C. J. AU - Raleigh, D. P. AU - Palmer III, A. G. JO - Journal of molecular biology PY - 2006 PB - Academic Press VL - 355 IS - 5 SP - 1078 EP - 1094 ER - TY - JOUR T1 - Coating single-walled carbon nanotubes with phospholipids AU - Wu, Y. AU - Hudson, J. S. AU - Lu, Q. AU - Moore, J. M. AU - Mount, A. S. AU - Rao, A. M. AU - Alexov, E. AU - Ke, P. C. JO - The Journal of Physical Chemistry B PY - 2006 PB - American Chemical Society VL - 110 IS - 6 SP - 2475 EP - 2478 ER - TY - JOUR T1 - Comparative study of the stability of poplar plastocyanin isoforms AU - Shosheva, A. AU - Donchev, A. AU - Dimitrov, M. AU - Kostov, G. AU - Toromanov, G. AU - Getov, V. AU - Alexov, E. JO - Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics PY - 2005 PB - Elsevier VL - 1748 IS - 1 SP - 116 EP - 127 ER - TY - JOUR T1 - Comparative study of generalized Born models: Born radii and peptide folding AU - Zhu, J. AU - Alexov, E. AU - Honig, B. JO - The Journal of Physical Chemistry B PY - 2005 PB - ACS Publications VL - 109 IS - 7 SP - 3008 EP - 3022 ER - TY - JOUR T1 - Modeling the First Electron Transfer from QA to QB AU - Alexov, E. AU - Gunner, M. JO - Molecular Bioenergetics: Simulations of Electron, Proton, and Energy Transfer PY - 2004 PB - Amer Chemical Society IS - 883 SP - 93 EP - 93 ER - TY - CHAP T1 - Modeling the First Electron Transfer from QA to QB in Reaction Center Proteins from Rb. sphaeroides AU - Alexov, E. AU - Gunner, M. PY - 2004 ER - TY - CHAP T1 - Use of limited suboptimal alignment in homology modeling AU - Tang, C. L. AU - Petrey, D. AU - Fasnacht, M. AU - Kosloff, M. AU - Alexov, E. AU - Honig, B. TI - Poster presented at 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB) PY - 2004 ER - TY - JOUR T1 - Experimental and numerical study of the poplar plastocyanin isoforms using Tyr as a probe for electrostatic similarity and dissimilarity AU - Shosheva, A. AU - Donchev, A. AU - Dimitrov, M. AU - Zlatanov, I. AU - Toromanov, G. AU - Getov, V. AU - Alexov, E. JO - Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics PY - 2004 PB - Elsevier VL - 1698 IS - 1 SP - 67 EP - 75 ER - TY - JOUR T1 - 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 AU - Alexov, E. JO - Proteins: Structure, Function, and Bioinformatics PY - 2004 PB - Wiley Online Library VL - 56 IS - 3 SP - 572 EP - 584 ER - TY - JOUR T1 - Numerical calculations of the pH of maximal protein stability: The effect of the sequence composition and three-dimensional structure AU - Alexov, E. JO - European Journal of Biochemistry PY - 2004 PB - Blackwell Science Ltd Oxford, UK VL - 271 IS - 1 SP - 173 EP - 185 ER - TY - CHAP T1 - Proton uptake/release induced by protein-inhibitor association. Application to pepstatin and plasmepsin, cathepsin D and endothiapepsin complexes. AU - Alexov, E. AU - Honig, B. TI - BIOPHYSICAL JOURNAL PY - 2003 VL - 84 IS - 2 SP - 505A EP - 505A ER - TY - JOUR T1 - Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: Comparing experimental with computed pKas AU - Alexov, E. JO - Proteins: Structure, Function, and Bioinformatics PY - 2003 PB - Wiley Online Library VL - 50 IS - 1 SP - 94 EP - 103 ER - TY - JOUR T1 - On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles AU - Tang, C. L. AU - Xie, L. AU - Koh, I. Y. AU - Posy, S. AU - Alexov, E. AU - Honig, B. JO - Journal of molecular biology PY - 2003 PB - Elsevier VL - 334 IS - 5 SP - 1043 EP - 1062 ER - TY - JOUR T1 - Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method AU - Rocchia, W. AU - Sridharan, S. AU - Nicholls, A. AU - Alexov, E. AU - Chiabrera, A. AU - Honig, B. JO - J Comp Chem PY - 2002 VL - 23 SP - 128 EP - 137 ER - TY - CHAP T1 - Perturbations of pKa in RNA structures: A survey using a Monte Carlo application of the NLPB equation AU - Tang, C. AU - Alexov, E. AU - Pyle, A. AU - Honig, B. TI - BIOPHYSICAL JOURNAL PY - 2002 VL - 82 IS - 1 SP - 131A EP - 131A ER - TY - CHAP T1 - The origins of pH dependent effects on protein stability: Applications to proteases AU - Alexov, E. AU - Honig, B. TI - Biophysical Journal PY - 2002 VL - 82 IS - 1 SP - 474A EP - 474A ER - TY - JOUR T1 - Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides AU - Tandori, J. AU - Maroti, P. AU - Alexov, E. AU - Sebban, P. AU - Baciou, L. JO - Proceedings of the National Academy of Sciences PY - 2002 PB - National Academy of Sciences VL - 99 IS - 10 SP - 6702 EP - 6706 ER - TY - JOUR T1 - Combining conformational flexibility and continuum electrostatics for calculating pKas in proteins AU - Georgescu, R. E. AU - Alexov, E. G. AU - Gunner, M. R. JO - Biophysical journal PY - 2002 PB - Cell Press VL - 83 IS - 4 SP - 1731 EP - 1748 ER - TY - JOUR T1 - 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 AU - Rocchia, W. AU - Sridharan, S. AU - Nicholls, A. AU - Alexov, E. AU - Chiabrera, A. AU - Honig, B. JO - Journal of computational chemistry PY - 2002 PB - Wiley Online Library VL - 23 IS - 1 SP - 128 EP - 137 ER - TY - JOUR T1 - Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions (vol 105B, pg 6507, 2001) AU - Rocchia, W. AU - Alexov, E. AU - Honig, B. JO - Journal of Physical Chemistry B PY - 2001 PB - American Chemical Society (ACS) VL - 105 IS - 28 SP - 6754 EP - 6754 ER - TY - JOUR T1 - ACCELERATED PUBLICATIONS-Revealing the involvement of extended hydrogen bond networks in the cooperative function between distant sites in bacterial reaction centers. AU - Tandori, J. AU - Baciou, L. AU - Alexov, E. AU - Maroti, P. AU - Schiffer, M. AU - Hanson, D. K. AU - Sebban, P. JO - Journal of Biological Chemistry PY - 2001 PB - Baltimore [etc.] VL - 276 IS - 49 SP - 45513 EP - 45515 ER - TY - JOUR T1 - ADDITIONS AND CORRECTIONS-Extending the Applicability of the Nonlinear Poisson-Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions AU - Rocchia, W. AU - Alexov, E. AU - Honig, B. JO - Journal of Physical Chemistry B-Condensed Phase PY - 2001 PB - Washington, DC: American Chemical Society, c1997- VL - 105 IS - 28 SP - 6754 EP - 6754 ER - TY - JOUR T1 - Revealing the involvement of extended hydrogen bond networks in the cooperative function between distant sites in bacterial reaction centers AU - Tandori, J. AU - Baciou, L. AU - Alexov, E. AU - Mar\'oti, P. AU - Schiffer, M. AU - Hanson, D. K. AU - Sebban, P. JO - Journal of Biological Chemistry PY - 2001 PB - Elsevier VL - 276 IS - 49 SP - 45513 EP - 45515 ER - TY - JOUR T1 - Extending the applicability of the nonlinear Poisson- Boltzmann equation: multiple dielectric constants and multivalent ions AU - Rocchia, W. AU - Alexov, E. AU - Honig, B. JO - The Journal of Physical Chemistry B PY - 2001 PB - American Chemical Society VL - 105 IS - 28 SP - 6507 EP - 6514 ER - TY - CHAP T1 - Modeling the free energy chances due to mutations of residues with multi conformation continuum electrostatic (MCCE) method: Application to reaction center proteins AU - Alexov, E. AU - Baciou, L. AU - Schiffer, M. AU - Sebban, P. AU - Hanson, D. AU - Gunner, M. TI - BIOPHYSICAL JOURNAL PY - 2000 VL - 78 IS - 1 SP - 31A EP - 31A ER - TY - CHAP T1 - Calculating the role of the protein in proton-and electron-transfer reactions. AU - Gunner, M. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2000 VL - 219 SP - U346 EP - U346 ER - TY - CHAP T1 - Reorganization of the QB pocket of photosynthetic reaction centers stabilizes ionization changes. AU - Gunner, M. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 2000 VL - 220 SP - U186 EP - U186 ER - TY - CHAP T1 - pK (a) calculations with conformational flexibility: the multi conformation continuum electrostatics procedure (MCCE) AU - Gunner, M. AU - Karpman, D. AU - Alexov, E. TI - Biophysical Journal PY - 2000 VL - 78 IS - 1 SP - 31A EP - 31A ER - TY - JOUR T1 - Modeling the effects of mutations on the free energy of the first electron transfer from QA-to QB in photosynthetic reaction centers AU - Alexov, E. AU - Miksovska, J. AU - Baciou, L. AU - Schiffer, M. AU - Hanson, D. AU - Sebban, P. AU - Gunner, M. JO - Biochemistry PY - 2000 PB - ACS Publications VL - 39 IS - 20 SP - 5940 EP - 5952 ER - TY - JOUR T1 - A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins AU - Gunner, M. AU - Alexov, E. JO - Biochimica et Biophysica Acta (BBA)-Bioenergetics PY - 2000 PB - Elsevier VL - 1458 IS - 1 SP - 63 EP - 87 ER - TY - CHAP T1 - Modeling the first electron transfer from QA to QB in reaction centers from the bacteria Rb. AU - Alexov, E. AU - Gunner, M. TI - Biophysical Journal PY - 1999 VL - 76 IS - 1 SP - A240 EP - A240 ER - TY - JOUR T1 - Calculated protein and proton motions coupled to electron transfer: electron transfer from QA-to QB in bacterial photosynthetic reaction centers AU - Alexov, E. AU - Gunner, M. JO - Biochemistry PY - 1999 PB - American Chemical Society VL - 38 IS - 26 SP - 8253 EP - 8270 ER - TY - CHAP T1 - Modeling motions in protiens that are coupled to electron tranfers. AU - Gunner, M. AU - Alexov, E. TI - ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY PY - 1998 VL - 216 SP - U159 EP - U159 ER - TY - JOUR T1 - Numerical simulation of aldolase tetramer stability AU - Miteva, M. AU - Alexov, E. AU - Atanasov, B. JO - European biophysics journal PY - 1998 PB - Springer-Verlag VL - 28 IS - 1 SP - 67 EP - 73 ER - TY - CHAP T1 - The Role of the Protein in Modulating Cofactor Electrochemistry in Proteins: The Calculation of Electrostatic Forces AU - Gunner, M. R. AU - Alexov, E. TI - Molecular Modeling and Dynamics of Bioinorganic Systems PY - 1997 PB - Springer, Dordrecht SP - 361 EP - 390 ER - TY - JOUR T1 - The importance of the protein in controlling the electrochemistry of heme metalloproteins: methods of calculation and analysis AU - Gunner, M. AU - Alexov, E. AU - Torres, E. AU - Lipovaca, S. JO - JBIC Journal of Biological Inorganic Chemistry PY - 1997 PB - Springer-Verlag VL - 2 IS - 1 SP - 126 EP - 134 ER - TY - JOUR T1 - Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties AU - Alexov, E. AU - Gunner, M. JO - Biophysical journal PY - 1997 PB - Cell Press VL - 72 IS - 5 SP - 2075 EP - 2093 ER - TY - JOUR T1 - Electrostatic interaction between two charged spherical molecules AU - Ohshima, H. AU - Mishonova, E. AU - Alexov, E. JO - Biophysical chemistry PY - 1996 PB - Elsevier VL - 57 IS - 23 SP - 189 EP - 203 ER - TY - CHAP T1 - Participant List AU - Alexandrov, V. AU - Alexov, E. G. AU - Andrec, M. AU - Apostolico, A. AU - Bhattacharya, A. AU - Brooks, D. J. AU - Cai, R. L. AU - Colasanti, A. AU - Ding, W. AU - Du, P. AU - others, TI - Proceedings of the Tsukuba Global Carbon Cycle Workshop--Global Environment Tsukuba'95: February 1-3, 1995, Tsukuba, Japan PY - 1995 SP - 169 EP - 169 ER - TY - JOUR T1 - Anisotropic behavior of the pH dependence part of Young's modulus in a lysozyme triclinic crystal AU - Alexov, E. AU - Atanasov, B. AU - Ueki, T. JO - Biopolymers: Original Research on Biomolecules PY - 1995 PB - Wiley Subscription Services, Inc., A Wiley Company Hoboken VL - 35 IS - 5 SP - 513 EP - 522 ER - TY - JOUR T1 - High-Frequency Backward Waves in Longitudinally Magnetized Gyrotropic Waveguides AU - Alexov, E. JO - Contributions to Plasma Physics PY - 1995 PB - WILEY-VCH Verlag Berlin VL - 35 IS - 1 SP - 23 EP - 32 ER - TY - JOUR T1 - Selective absorption of radio frequency energy due to collective motion of charged domains: case of lysozyme crystal AU - Alexov, E. AU - Atanasov, B. JO - Journal of Biomolecular Structure and Dynamics PY - 1995 PB - Taylor \& Francis Group VL - 13 IS - 2 SP - 219 EP - 228 ER - TY - JOUR T1 - Cherenkov generation of Rayleigh electromagnetic wave in a gyrotropic plasma waveguide AU - Ivanov, S. AU - Alexov, E. JO - Nuclear Instruments and Methods in Physics Research A PY - 1994 VL - 341 IS - 1 SP - ABS109 EP - ABS110 ER - TY - JOUR T1 - Modeling of the electrostatic potential created by a spherical molecule AU - Alexov, E. AU - Mishonova, E. JO - Journal of Macromolecular Science, Part B PY - 1994 PB - Taylor \& Francis Group VL - 33 IS - 1 SP - 21 EP - 35 ER - TY - JOUR T1 - Analysis of electrostatic interactions in ribonuclease A monoclinic crystal AU - Alexov, E. AU - Atanasov, B. JO - Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology PY - 1994 PB - Elsevier VL - 1206 IS - 1 SP - 55 EP - 62 ER - TY - JOUR T1 - Rejection band in waveguide filled with cold magnetoactive plasma AU - Alexov, E. G. AU - Ivanov, S. T. AU - Kapchinskii, M. I. JO - Japanese journal of applied physics PY - 1994 PB - IOP Publishing VL - 33 IS - 5 SP - 2730 EP - 2730 ER - TY - JOUR T1 - Polaritons along the interface between an anisotropic semiconductor and a metallic screen AU - Ivanov, S. T. AU - Ivanova, K. AU - Alexov, E. JO - Physica Scripta PY - 1994 PB - IOP Publishing VL - 49 IS - 2 SP - 228 EP - 228 ER - TY - JOUR T1 - Rayleigh surface waves along the boundary between a plasma and a metallic screen AU - Ivanov, S. AU - Ivanova, K. AU - Alexov, E. JO - Journal of plasma physics PY - 1993 PB - Cambridge University Press VL - 49 IS - 2 SP - 227 EP - 235 ER - TY - JOUR T1 - Nonreciprocal effects in a plasma waveguide AU - Alexov, E. G. AU - Ivanov, S. T. JO - IEEE transactions on plasma science PY - 1993 PB - IEEE VL - 21 IS - 2 SP - 254 EP - 257 ER - TY - JOUR T1 - An additional solution of the waveguide problem for a waveguide partially filled with a magnetoactive semiconductor plasma AU - Alexov, E. JO - Physica Scripta PY - 1992 PB - IOP Publishing VL - 46 IS - 5 SP - 429 EP - 429 ER - TY - JOUR T1 - Anisotropic TEM-mode in a plasma waveguide AU - Alexov, E. AU - Ivanov, S. JO - Sov. J. Plasma Phys.(USA) PY - 1990 VL - 16 SP - 283 EP - 283 ER - TY - JOUR T1 - Surface wave evolution in a waveguide with an axial plasma column upon changing the external magnetic field AU - Ivanov, S. AU - Alexov, E. AU - Bogdanov, A. AU - Malinov, P. JO - Plasma physics and controlled fusion PY - 1990 PB - IOP Publishing VL - 32 IS - 10 SP - 791 EP - 791 ER - TY - JOUR T1 - Electromagnetic waves in waveguide partially filled with semiconductor plasma AU - Ivanov, S. AU - Alexov, E. JO - Contributions to Plasma Physics PY - 1990 PB - WILEY-VCH Verlag Berlin VL - 30 IS - 6 SP - 763 EP - 774 ER - TY - JOUR T1 - Waveguide partially filled with semiconductor plasma AU - Ivanov, S. AU - Alexov, E. AU - Malinov, P. JO - Physica Scripta PY - 1990 PB - IOP Publishing VL - 42 IS - 4 SP - 452 EP - 452 ER - TY - JOUR T1 - Nonsymmetrical Electromagnetic Waves in Partially Plasma—Filled Waveguide AU - Ivanov, S. AU - Alexov, E. AU - Malinov, P. JO - Contributions to Plasma Physics PY - 1990 PB - WILEY-VCH Verlag Berlin VL - 30 IS - 6 SP - 755 EP - 762 ER - TY - JOUR T1 - A new family of electromagnetic waves in a waveguide filled with magnetoactive semiconductor plasma AU - Ivanov, S. AU - Bogdanov, A. AU - Alexov, E. JO - Physica Scripta PY - 1990 PB - IOP Publishing VL - 42 IS - 4 SP - 458 EP - 458 ER - TY - JOUR T1 - Electromagnetic waves in a plasma waveguide AU - Ivanov, S. AU - Alexov, E. JO - Journal of plasma Physics PY - 1990 PB - Cambridge University Press VL - 43 IS - 1 SP - 51 EP - 67 ER - TY - JOUR T1 - Electromagnetic waven in fully-filled plasma waveguide AU - Ivanov, S. AU - Alexov, E. JO - J. of Plasma PY - 1989 VL - 15 SP - 1131 EP - 1131 ER - TY - JOUR T1 - Electromagnetic waves in the semiconductor plasma waveguide AU - Ivanov, S. AU - Alexov, E. JO - Physica Scripta PY - 1989 PB - IOP Publishing VL - 40 IS - 1 SP - 58 EP - 58 ER - TY - JOUR T1 - Symmetrical electromagnetic waves in partially-filled plasma waveguide AU - Ivanov, S. AU - Alexov, E. AU - Malinov, P. JO - Plasma physics and controlled fusion PY - 1989 PB - IOP Publishing VL - 31 IS - 6 SP - 941 EP - 941 ER -