Y. Shao, M. McGowan, S. Wang, E. Alexov, and S. Zhao. Convergence of a diffuse interface Poisson-Boltzmann (pb) model to the sharp interface pb model: a unified regularization formulation. Applied Mathematics and Computation, volume 436, pages 127501, 2023.

S. Sun, P. Poudel, E. Alexov, and L. Li. Electrostatics in Computational Biophysics and Its Implications for Disease Effects. International Journal of Molecular Sciences, volume 23, issue 18, pages 10347, 2022.

S. Panday and E. Alexov. Protein–Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation. ACS omega, volume 7, issue 13, pages 11057-11067, 2022.

S. Wang, Y. Shao, E. Alexov, and S. Zhao. A regularization approach for solving the super-Gaussian Poisson-Boltzmann model with heterogeneous dielectric functions. Journal of Computational Physics, pages 111340, 2022.

R. Aprigliano, S. Bradamante, B. Mihaljevic, W. Wang, S. L. F. Martin, D. L. Bordin, M. Bosshard, N. P. Montaldo, Y. Peng, E. Alexov, and others. Increased p53 signaling impairs neural differentiation causing HUWE1-promoted intellectual disabilities. Cell Reports Medicine, Cold Spring Harbor Laboratory, volume 2, pages 100240, April 2021.

M. Koirala, H. Shashikala, J. Jeffries, B. Wu, S. K. Loftus, J. H. Zippin, and E. Alexov. Computational Investigation of the pH Dependence of Stability of Melanosome Proteins: Implication for Melanosome formation and Disease. International journal of molecular sciences, Multidisciplinary Digital Publishing Institute, volume 22, issue 15, pages 8273, 2021.

E. Alexov. Special Issue on Computational Chemistry Methods to Predict pKa’s of Ionizable Groups in Proteins, RNAs, DNAs and Small Molecules. Journal of Computational Biophysics and Chemistry, volume 20, issue 2, pages 109-110, 2021.

G. Li, S. Panday, Y. Peng, and E. Alexov. SAMPDI-3D: predicting the effects of protein and DNA mutations on protein-DNA interactions. Bioinformatics (Oxford, England), 2021.

B. Wu, W. Hand, and E. Alexov. Opioid Addiction and Opioid Receptor Dimerization: Structural Modeling of the OPRD1 and OPRM1 Heterodimer and Its Signaling Pathways. International journal of molecular sciences, Multidisciplinary Digital Publishing Institute (MDPI), volume 22, issue 19, 2021.

S. Wang, E. Alexov, and S. Zhao. On regularization of charge singularities in solving the Poisson-Boltzmann equation with a smooth solute-solvent boundary [J]. Mathematical Biosciences and Engineering, volume 18, issue 2, pages 1370-1405, 2021.

G. Li, S. K. Panday, and E. Alexov. SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability. International Journal of Molecular Sciences, Multidisciplinary Digital Publishing Institute, volume 22, issue 2, pages 606, 2021.

H. Shashikala, A. Chakravorty, S. K. Panday, and E. Alexov. BION-2: Predicting Positions of Non-Specifically Bound Ions on Protein Surface by a Gaussian-Based Treatment of Electrostatics. International Journal of Molecular Sciences, Multidisciplinary Digital Publishing Institute, volume 22, issue 1, pages 272, 2021.

B. Wu, W. Hand, and E. Alexov. Opioid addiction and opioid receptor dimerization: structural modeling of the OPRD1 and OPRM1 heterodimer and its signaling pathways. International journal of molecular sciences, volume 22, issue 19, pages 10290, 2021.

G. Li, S. Panday, Y. Peng, and E. Alexov. SAMPDI-3D: predicting the effects of protein and DNA mutations on protein–DNA interactions. Bioinformatics, volume 37, issue 21, pages 3760-3765, 2021.

E. Alexov. Special Issue on Computational Chemistry Methods to Predict pKa’s of Ionizable Groups in Proteins, RNAs, DNAs and Small Molecules. Journal of Computational Biophysics and Chemistry, volume 2, issue 2, pages 109-110, 2021.

E. Alexov. Towards More Biology-Oriented Papers: Name Change of the Journal of Theoretical and Computational Chemistry to Journal of Computational Biophysics and Chemistry. Journal of Computational Biophysics and Chemistry, World Scientific Publishing Company, volume 20, issue 1, pages 1, 2021.

E. Alexov and others. An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants. Genes, volume 11, issue 9, 2020.

C. Li, M. McGowan, E. Alexov, and S. Zhao. A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation [J]. Mathematical Biosciences and Engineering, volume 17, issue 6, pages 6259-6277, 2020.

S. R. Ganakammal and E. Alexov. An Ensemble Approach to Predict the Pathogenicity of Synonymous Variants. Genes, Multidisciplinary Digital Publishing Institute, volume 11, issue 9, pages 1102, 2020.

G. Li, S. Pahari, A. K. Murthy, S. Liang, R. Fragoza, H. Yu, and E. Alexov. SAAMBE-SEQ: a sequence-based method for predicting mutation effect on protein--protein binding affinity. Bioinformatics, 2020.

M. Koirala and E. Alexov. Ab-initio binding of barnase--barstar with DelPhiForce steered Molecular Dynamics (DFMD) approach. Journal of Theoretical and Computational Chemistry, World Scientific Publishing Company, volume 19, issue 4, pages 2050016, 2020.

Y. Peng, R. Kelle, C. Little, E. Michonova, K. G. Kornev, and E. Alexov. pH-dependent interactions of Apolipophorin-III with a lipid disk. Journal of Computational Biophysics and Chemistry, World Scientific Publishing Company, pages 1-12, 2020.

S. R. Ganakammal, M. Koirala, B. Wu, and E. Alexov. In-silico analysis to identify the role of MEN1 missense mutations in breast cancer. Journal of Theoretical and Computational Chemistry, World Scientific Publishing Company, volume 19, issue 6, pages 2041002, 2020.

S. Pahari, G. Li, A. K. Murthy, S. Liang, R. Fragoza, H. Yu, and E. Alexov. SAAMBE-3D: Predicting effect of mutations on protein--protein interactions. International journal of molecular sciences, Multidisciplinary Digital Publishing Institute, volume 21, issue 7, pages 2563, 2020.

A. Chakravorty, S. Panday, S. Pahari, S. Zhao, and E. Alexov. Capturing the Effects of Explicit Waters in Implicit Electrostatics Modeling: Qualitative Justification of Gaussian-Based Dielectric Models in DelPhi. Journal of chemical information and modeling, American Chemical Society, volume 60, issue 4, pages 2229-2246, 2020.

M. Koirala and E. Alexov. Computational Analysis of Missense Mutations in Creatine Transporter Protein Associated with Creatine Deficiency Syndrome. Biophysical Journal, Elsevier, volume 118, issue 3, pages 197a, 2020.

S. Wang, A. Lee, E. Alexov, and S. Zhao. A regularization approach for solving Poisson’s equation with singular charge sources and diffuse interfaces. Applied Mathematics Letters, Pergamon, volume 102, pages 106144, 2020.

M. Koirala and E. Alexov. Computational chemistry methods to investigate the effects caused by DNA variants linked with disease. Journal of Theoretical and Computational Chemistry, World Scientific Publishing Company, volume 19, issue 6, pages 1930001, 2020.

S. Pahari and E. Alexov. Modeling pKa without solute-water boundary: DelPhiPKa and its applications to protein-protein binding. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 258, 2019.

A. Chakravorty, J. Higham, E. Alexov, and R. Henchman. Effect of water on the entropy of protein-protein binding. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 258, 2019.

S. K. Panday, M. H. Shashikala, A. Chakravorty, S. Zhao, and E. Alexov. Reproducing ensemble averaged electrostatics with Super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes. Communications in Information and Systems, volume 19, issue 4, 2019.

S. R. Ganakammal and E. Alexov. Evaluation of performance of leading algorithms for variant pathogenicity predictions and designing a combinatory predictor method: Application to Rett syndrome variants. PeerJ, PeerJ Inc., volume 7, pages e8106, 2019.

S. K. Panday, M. H. Shashikala, M. Koirala, S. Pahari, A. Chakvorty, Y. Peng, L. Li, Z. Jia, C. Li, and E. Alexov. Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]. Living Journal of Computational Molecular Science, University of Colorado Boulder, volume 1, issue 2, pages 10841, 2019.

B. Wu, Y. Peng, J. Eggert, and E. Alexov. Novel Genetic Markers for Early Detection of Elevated Breast Cancer Risk in Women. International journal of molecular sciences, Multidisciplinary Digital Publishing Institute, volume 20, issue 19, pages 4828, 2019.

H. Shashikala, A. Chakravorty, and E. Alexov. Modeling electrostatic force in protein-protein recognition. Frontiers in molecular biosciences, Frontiers, volume 6, pages 94, 2019.

Y. Peng, Y. Yang, L. Li, Z. Jia, W. Cao, and E. Alexov. DFMD: fast and effective DelPhiForce steered molecular dynamics approach to model ligand approach toward a receptor: Application to spermine synthase enzyme. Frontiers in molecular biosciences, Frontiers, volume 6, pages 74, 2019.

N. Tajielyato and E. Alexov. Modeling pKas of unfolded proteins to probe structural models of unfolded state. Journal of Theoretical and Computational Chemistry, World Scientific Publishing Company, volume 18, issue 4, pages 1950020, 2019.

T. Hazra, S. A. Ullah, S. Wang, E. Alexov, and S. Zhao. A super-Gaussian Poisson--Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states. Journal of mathematical biology, Springer Berlin Heidelberg, volume 79, issue 2, pages 631-672, 2019.

C. J. Spellicy, Y. Peng, L. Olewiler, S. S. Cathey, R. C. Rogers, D. Bartholomew, J. Johnson, E. Alexov, J. A. Lee, M. J. Friez, and others. Three additional patients with EED-associated overgrowth: potential mutation hotspots identified? Journal of human genetics, Nature Publishing Group, volume 64, issue 6, pages 561-572, 2019.

N. Tajielyato and E. Alexov. Processivity vs. beating: Comparing cytoplasmic and axonemal dynein microtubule binding domain association with microtubule. International journal of molecular sciences, Multidisciplinary Digital Publishing Institute, volume 20, issue 5, pages 1090, 2019.

S. Pahari, L. Sun, and E. Alexov. PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. Database, Oxford Academic, volume 2019, 2019.

M. S. H. Bosthanthirige, A. Chakravorty, and E. Alexov. Modeling Electrostatic Force in Protein-Protein Recognition. Biophysical Journal, Elsevier, volume 116, issue 3, pages 46a, 2019.

A. Chakravorty, J. Higham, E. Alexov, and R. H. Henchman. New method to determine the effect of dimerization on protein flexibility from molecular dynamics simulation using structural hierarchy. Biophysical Journal, Elsevier, volume 116, issue 3, pages 561a-562a, 2019.

N. Tajielyato, J. Alper, and E. Alexov. Comparative Study of Flagellar and Cytoplasmic Dyneins. Biophysical Journal, Elsevier, volume 116, issue 3, pages 560a, 2019.

S. Pahari, L. Sun, and E. Alexov. Surface-Free Protocol for Computing PKA's (DelPhiPKa): Applications to Protein-Protein Interactions. Biophysical Journal, Elsevier, volume 116, issue 3, pages 166a, 2019.

B. Wu, Y. Peng, J. A. Eggert, and E. Alexov. Investigating the Effects of Missense Mutations in MSH2 Gene Associated with Lynch Syndrome. Biophysical Journal, Elsevier, volume 116, issue 3, pages 192a, 2019.

Y. Peng, M. Koirala, and E. Alexov. Electrostatic Force Driven Molecular Dynamics Simulations. Biophysical Journal, Elsevier, volume 116, issue 3, pages 290a, 2019.

A. Chakravorty, E. Gallicchio, and E. Alexov. A grid-based algorithm in conjunction with a gaussian-based model of atoms for describing molecular geometry. Journal of computational chemistry, John Wiley \& Sons, Inc. Hoboken, USA, volume 40, issue 12, pages 1290-1304, 2019.

Y. Peng, E. Alexov, and S. Basu. Structural perspective on revealing and altering molecular functions of genetic variants linked with diseases. International journal of molecular sciences, Multidisciplinary Digital Publishing Institute, volume 20, issue 3, pages 548, 2019.

Y. Peng, E. Alexov, and S. Basu. Structural Perspective on Revealing and Altering Molecular Mechanisms of Genetic Variants Linked with Diseases. 2018.

N. Tajielyato, J. Alper, and E. Alexov. Modeling Tubulin E-Hooks Interactions with Dynein Microtubule Binding Domain. PROTEIN SCIENCE, volume 27, pages 198-198, 2018.

S. Pahari, L. Sun, S. Basu, and E. Alexov. DelPhiPKa: Including salt in the calculations and enabling polar residues to titrate. Proteins: Structure, Function, and Bioinformatics, John Wiley \& Sons, Inc. Hoboken, USA, volume 86, issue 12, pages 1277-1283, 2018.

N. Tajielyato, L. Li, Y. Peng, J. Alper, and E. Alexov. E-hooks provide guidance and a soft landing for the microtubule binding domain of dynein. Scientific reports, Nature Publishing Group, volume 8, issue 1, pages 1-10, 2018.

A. Chakravorty, Z. Jia, Y. Peng, N. Tajielyato, L. Wang, and E. Alexov. Gaussian-based smooth dielectric function: a surface-free approach for modeling macromolecular binding in solvents. Frontiers in molecular biosciences, Frontiers, volume 5, pages 25, 2018.

Z. Jia, L. Li, Y. Peng, F. Ding, and E. Alexov. The capricious electrostatic force: Revealing the signaling pathway in integrin $\alpha$ 2-I domain. Journal of Theoretical and Computational Chemistry, World Scientific Publishing Company, volume 17, issue 3, pages 1840001, 2018.

S. C. Godar, H. Lovelace, J. Eller, M. Spencer, L. Li, G. Hamilton, H. Sanabria, E. Alexov, and J. Alper. Single Molecule Study of Long-Range Electrostatic Binding Affinity of Cytoplasmic Dynein's Microtubule Binding Domain. Biophysical Journal, Elsevier, volume 114, issue 3, pages 512a, 2018.

C. J. Spellicy, J. Norris, R. Bend, C. Bupp, P. Mester, T. Reynolds, J. Dean, Y. Peng, E. Alexov, C. E. Schwartz, and others. Key apoptotic genes APAF1 and CASP9 implicated in recurrent folate-resistant neural tube defects. European Journal of Human Genetics, Nature Publishing Group, volume 26, issue 3, pages 420-427, 2018.

A. Chakravorty, Z. Jia, L. Li, S. Zhao, and E. Alexov. Reproducing the ensemble average polar solvation energy of a protein from a single structure: gaussian-based smooth dielectric function for macromolecular modeling. Journal of chemical theory and computation, American Chemical Society, volume 14, issue 2, pages 1020-1032, 2018.

Y. Peng, R. Myers, W. Zhang, and E. Alexov. Computational investigation of the missense mutations in DHCR7 gene associated with Smith-Lemli-Opitz syndrome. International journal of molecular sciences, Multidisciplinary Digital Publishing Institute, volume 19, issue 1, pages 141, 2018.

Y. Peng, L. Sun, Z. Jia, L. Li, and E. Alexov. Predicting protein--DNA binding free energy change upon missense mutations using modified MM/PBSA approach: SAMPDI webserver. Bioinformatics, Oxford University Press, volume 34, issue 5, pages 779-786, 2018.

Z. Jia and E. Alexov. Simulation study of integrin alpha-2 I domain activation. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 254, 2017.

Y. Peng and E. Alexov. Predicting binding free energy change caused by missense mutations in protein-DNA interactions using modified MM/PBSA method. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 254, 2017.

L. Li, Z. Jia, Y. Peng, S. Godar, I. Getov, S. Teng, J. Alper, and E. Alexov. Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations. Scientific reports, Nature Publishing Group, volume 7, issue 1, pages 1-12, 2017.

Y. Peng and E. Alexov. Protein Conformational Disease: Visit the Facts at a Glance. eLS, American Cancer Society, pages 1-7, 2017.

L. Li, Z. Jia, Y. Peng, A. Chakravorty, L. Sun, and E. Alexov. DelPhiForce web server: electrostatic forces and energy calculations and visualization. Bioinformatics, Oxford University Press, volume 33, issue 22, pages 3661-3663, 2017.

Z. Jia, L. Li, A. Chakravorty, and E. Alexov. Treating ion distribution with G aussian-based smooth dielectric function in DelPhi. 2017.

L. Hoffman, L. Li, E. Alexov, H. Sanabria, and M. N. Waxham. Cytoskeletal-like Filaments of Ca2+-Calmodulin-Dependent Protein Kinase II Are Formed in a Regulated and Zn2+-Dependent Manner. Biochemistry, American Chemical Society, volume 56, issue 15, pages 2149-2160, 2017.

A. Chakravorty, Z. Jia, L. Li, and E. Alexov. A new DelPhi feature for modeling electrostatic potential around proteins: Role of bound ions and implications for zeta-potential. Langmuir, American Chemical Society, volume 33, issue 9, pages 2283-2295, 2017.

L. Hoffman, L. Li, E. Alexov, M. N. Waxham, and H. Sanabria. Calcium Calmodulin Regulates Zinc Mediated Changes in the Structure, Self-Association, and Activity of CaMKII. Biophysical Journal, Elsevier, volume 112, issue 3, pages 444a-445a, 2017.

L. Li, J. Alper, and E. Alexov. Multi-Scale Investigation on the Mechanisms of Dyneins’ Motion on Microtubule. Biophysical Journal, Elsevier, volume 112, issue 3, pages 261a, 2017.

L. Li, A. Chakravorty, and E. Alexov. DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. Journal of computational chemistry, volume 38, issue 9, pages 584-593, 2017.

Y. Peng and E. Alexov. Computational investigation of proton transfer, p K a shifts and p H-optimum of protein--DNA and protein--RNA complexes. Proteins: Structure, Function, and Bioinformatics, volume 85, issue 2, pages 282-295, 2017.

E. Alexov. Parallelization schemes for solving Poisson-Boltzmann equation via finite-difference method: Implementations in DelPhi and applications. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 252, 2016.

B. Campbell, L. Li, and E. Alexov. Dielectric Properties of Biological Macromolecules and Biomolecule--Water Interfaces. Encyclopedia of Biocolloid and Biointerface Science 2V Set, John Wiley \& Sons, Inc. Hoboken, NJ, USA, pages 380-390, 2016.

Y. Peng and E. Alexov. Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model. Proteins: Structure, Function, and Bioinformatics, volume 84, issue 12, pages 1797-1809, 2016.

A. Chakavorty, L. Li, and E. Alexov. Electrostatic component of binding energy: interpreting predictions from poisson--boltzmann equation and modeling protocols. Journal of computational chemistry, volume 37, issue 28, pages 2495-2507, 2016.

L. Li, J. Alper, and E. Alexov. Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions. Scientific reports, Nature Publishing Group, volume 6, issue 1, pages 1-12, 2016.

Y. Yang, T. G. Kucukkal, J. Li, E. Alexov, and W. Cao. Binding analysis of methyl-CpG binding domain of MeCP2 and Rett syndrome mutations. ACS chemical biology, American Chemical Society, volume 11, issue 10, pages 2706-2715, 2016.

M. Petukh, L. Dai, and E. Alexov. SAAMBE: webserver to predict the charge of binding free energy caused by amino acids mutations. International journal of molecular sciences, Multidisciplinary Digital Publishing Institute, volume 17, issue 4, pages 547, 2016.

Y. Peng, J. Norris, C. Schwartz, and E. Alexov. Revealing the effects of missense mutations causing Snyder-Robinson syndrome on the stability and dimerization of spermine synthase. International journal of molecular sciences, Multidisciplinary Digital Publishing Institute, volume 17, issue 1, pages 77, 2016.

I. Getov, M. Petukh, and E. Alexov. SAAFEC: predicting the effect of single point mutations on protein folding free energy using a knowledge-modified MM/PBSA approach. International journal of molecular sciences, Multidisciplinary Digital Publishing Institute, volume 17, issue 4, pages 512, 2016.

L. Li, J. Alper, and E. Alexov. Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules. Scientific reports, Nature Publishing Group, volume 6, issue 1, pages 1-12, 2016.

L. Wang, M. Zhang, and E. Alexov. DelPhiPKa web server: predicting p K a of proteins, RNAs and DNAs. Bioinformatics, Oxford University Press, volume 32, issue 4, pages 614-615, 2016.

Y. Peng and E. Alexov. Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding. Proteins: Structure, Function, and Bioinformatics, volume 84, issue 2, pages 232-239, 2016.

I. Getov, M. Petukh, and E. Alexov. Predicting folding free energy changes caused by single point mutations via combined usage of MM-PBSA method and biophysical characteristics. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 250, 2015.

E. Alexov. Navigating through genomics data to deliver testable predictions. Human Mutation, volume 36, issue 2, pages v-v, 2015.

M. Petukh, J. Morrison, M. Li, A. Panchenko, and E. Alexov. SAMBE: The New Webserver for Predicting the Effect of nssNP on the Protein-Protein Binding Free Energy. Biophysical Journal, Elsevier, volume 108, issue 2, pages 157a-158a, 2015.

M. Petukh, M. Zhang, and E. Alexov. Statistical investigation of surface bound ions and further development of BION server to include p H and salt dependence. Journal of computational chemistry, volume 36, issue 32, pages 2381-2393, 2015.

T. G. Kucukkal and E. Alexov. Structural, dynamical, and energetical consequences of Rett syndrome mutation R133C in MeCP2. Computational and mathematical methods in medicine, Hindawi, volume 2015, 2015.

T. G. Kucukkal, Y. Yang, O. Uvarov, W. Cao, and E. Alexov. Impact of rett syndrome mutations on MeCP2 MBD stability. Biochemistry, American Chemical Society, volume 54, issue 41, pages 6357-6368, 2015.

Y. Peng, J. Suryadi, Y. Yang, T. G. Kucukkal, W. Cao, and E. Alexov. Mutations in the KDM5C ARID domain and their plausible association with syndromic Claes-Jensen-Type disease. International journal of molecular sciences, Multidisciplinary Digital Publishing Institute, volume 16, issue 11, pages 27270-27287, 2015.

L. Li, L. Wang, and E. Alexov. On the energy components governing molecular recognition in the framework of continuum approaches. Frontiers in molecular biosciences, Frontiers, volume 2, pages 5, 2015.

M. Petukh, M. Li, and E. Alexov. Predicting binding free energy change caused by point mutations with knowledge-modified MM/PBSA method. PLoS computational biology, Public Library of Science San Francisco, CA USA, volume 11, issue 7, pages e1004276, 2015.

L. Wang, L. Li, and E. Alexov. pKa predictions for proteins, RNA s, and DNA s with the Gaussian dielectric function using DelPhi pKa. Proteins: Structure, Function, and Bioinformatics, volume 83, issue 12, pages 2186-2197, 2015.

M. Petukh, T. G. Kucukkal, and E. Alexov. On human disease-causing amino acid variants: Statistical study of sequence and structural patterns. Human mutation, volume 36, issue 5, pages 524-534, 2015.

T. G. Kucukkal, M. Petukh, L. Li, and E. Alexov. Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins. Current opinion in structural biology, Elsevier Current Trends, volume 32, pages 18-24, 2015.

E. Alexov and R. Luo. Electrostatics and polarization effects in biophysical chemistry: in silico and in vitro. WORLD SCIENTIFIC PUBL CO PTE LTD 5 TOH TUCK LINK, SINGAPORE 596224, SINGAPORE, 2014.

Z. Zhang, V. Martiny, D. Lagorce, Y. Ikeguchi, E. Alexov, and others. Rational Design of Small-Molecule Stabilizers of Spermine Synthase Dimer by Virtual. 2014.

L. Li, N. Smith, and E. Alexov. Modeling ensemble-averaged electrostatics with smooth Gaussian-based dielectric function. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 248, 2014.

B. Wu, J. Eggert, and E. Alexov. Molecular mechanisms underlying pathogenic missense mutations. eLS, American Cancer Society, 2014.

B. Campbell, M. Petukh, E. Alexov, and C. Li. On the electrostatic properties of homodimeric proteins. Journal of Theoretical and Computational Chemistry, World Scientific Publishing Company, volume 13, issue 3, pages 1440007, 2014.

M. Petukh and E. Alexov. Ion binding to biological macromolecules. Asian journal of physics: an international quarterly research journal, NIH Public Access, volume 23, issue 5, pages 735, 2014.

P. Nedumpully-Govindan, L. Li, E. G. Alexov, M. A. Blenner, and F. Ding. Structural and energetic determinants of tyrosylprotein sulfotransferase sulfation specificity. Bioinformatics, Oxford University Press, volume 30, issue 16, pages 2302-2309, 2014.

E. Alexov. Advances in human biology: combining genetics and molecular biophysics to pave the way for personalized diagnostics and medicine. Advances in Biology, Hindawi, volume 2014, 2014.

M. Petukh, B. Wu, S. Stefl, N. Smith, D. Hyde-Volpe, L. Wang, and E. Alexov. Chronic beryllium disease: revealing the role of beryllium ion and small peptides binding to HLA-DP2. PLoS One, Public Library of Science, volume 9, issue 11, pages e111604, 2014.

T. Kimmett, N. Smith, S. Witham, M. Petukh, S. Sarkar, and E. Alexov. ProBLM web server: protein and membrane placement and orientation package. Computational and mathematical methods in medicine, Hindawi, volume 2014, 2014.

R. P. Dias, L. Li, T. A. Soares, and E. Alexov. Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: the MEMPOT algorithm implemented in DelPhi. Journal of computational chemistry, volume 35, issue 19, pages 1418-1429, 2014.

L. Li, C. Li, and E. Alexov. On the modeling of polar component of solvation energy using smooth Gaussian-based dielectric function. Journal of Theoretical and Computational Chemistry, World Scientific Publishing Company, volume 13, issue 3, pages 1440002, 2014.

Z. Zhang, V. Martiny, D. Lagorce, Y. Ikeguchi, E. Alexov, and M. A. Miteva. Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach. PLoS One, Public Library of Science, volume 9, issue 10, pages e110884, 2014.

N. Dolzhanskaya, M. A. Gonzalez, F. Sperziani, S. Stefl, J. Messing, G. Y. Wen, E. Alexov, S. Zuchner, and M. Velinov. 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. Journal of Alzheimer's Disease, IOS Press, volume 39, issue 1, pages 23-27, 2014.

T. G. Kucukkal, Y. Yang, S. C. Chapman, W. Cao, and E. Alexov. Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics. International journal of molecular sciences, Multidisciplinary Digital Publishing Institute, volume 15, issue 6, pages 9670-9717, 2014.

M. Li, M. Petukh, E. Alexov, and A. R. Panchenko. Predicting the impact of missense mutations on protein--protein binding affinity. Journal of chemical theory and computation, American Chemical Society, volume 10, issue 4, pages 1770-1780, 2014.

E. Alexov. Electrostatics and polarization effects in biophysical chemistry: In silico, in vitro, and in vivo. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 246, 2013.

M. Petukh, A. Panchenko, and E. Alexov. Electrostatics plays significant role in changes of the protein-protein affinity due to missense mutations. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 246, 2013.

L. Li, C. Li, and E. Alexov. Smooth dielectric function for modeling electrostatics in biological macromolecules. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 246, 2013.

C. Li, M. Petukh, L. Li, and E. Alexov. Multi-Level and Interleaved Poisson-Boltzmann (MLIPB) Method for Parallel Computing of the Electrostatics and its Application in Delphi. Biophysical Journal, Elsevier, volume 104, issue 2, pages 507a, 2013.

K. Vaidyanathan, T. Niranjan, M. May, R. Rose, C. F. Teo, S. Prabakaran, R. Bridger, E. Alexov, T. Wang, C. Schwartz, and others. Characterizing a missense mutation in O-GlcNAc transferase that segregates with disease in a family with X-linked Intellectual Disability. GLYCOBIOLOGY, volume 23, issue 11, pages 1334-1335, 2013.

Z. Zhang, V. Martiny, D. Lagorce, E. Alexov, M. Miteva, and others. Snyder-Robinson Syndrome: Rescuing the Disease-Causing Effect of G56S mutant by Small Molecule Binding. APS March Meeting Abstracts, volume 2013, pages G45-005, 2013.

L. Li, C. Li, and E. Alexov. Modeling Proteins and Small Molecules with Inhomogeneous Dielectric Function: Implementation in Delphi. Biophysical Journal, Elsevier, volume 104, issue 2, pages 35a, 2013.

E. Alexov and G.-W. Wei. Preface: Special Issue on Modeling Electrostatics in Molecular Biology (MEMB). Communications in Computational Physics, Cambridge University Press, volume 13, issue 1, pages i-v, 2013.

Z. Zhang, A. Pegg, Y. Ikeguchi, and E. Alexov. Enhancing Human Spermine Synthase Activity by Site Directed Mutations. Biophysical Journal, Elsevier, volume 104, issue 2, pages 380a, 2013.

M. Petukh, C. Li, and E. Alexov. Predicting non-specifically bound ions: Application to BION webserver and beryllium disease. Biophysical Journal, Elsevier, volume 104, issue 2, pages 506a, 2013.

M. Petukh, T. Kimmet, and E. Alexov. BION web server: predicting non-specifically bound surface ions. Bioinformatics, Oxford University Press, volume 29, issue 6, pages 805-806, 2013.

E. Alexov and M. Sternberg. Understanding molecular effects of naturally occurring genetic differences. Journal of molecular biology, volume 425, issue 21, pages 3911-3913, 2013.

C. Li, M. Petukh, L. Li, and E. Alexov. Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi. Journal of computational chemistry, Wiley Online Library, volume 34, issue 22, pages 1949-1960, 2013.

L. Wang, S. Witham, Z. Zhang, L. Li, M. E. Hodsdon, and E. Alexov. In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor. Communications in computational physics, NIH Public Access, volume 13, issue 1, pages 207, 2013.

Z. Zhang, S. Witham, M. Petukh, G. Moroy, M. Miteva, Y. Ikeguchi, and E. Alexov. A rational free energy-based approach to understanding and targeting disease-causing missense mutations. Journal of the American Medical Informatics Association, BMJ Publishing Group BMA House, Tavistock Square, London, WC1H 9JR, volume 20, issue 4, pages 643-651, 2013.

Z. Zhang, Y. Zheng, M. Petukh, A. Pegg, Y. Ikeguchi, and E. Alexov. Enhancing human spermine synthase activity by engineered mutations. PLoS Comput Biol, Public Library of Science, volume 9, issue 2, pages e1002924, 2013.

S. Sarkar, S. Witham, J. Zhang, M. Zhenirovskyy, W. Rocchia, and E. Alexov. DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes. Communications in computational physics, NIH Public Access, volume 13, issue 1, pages 269, 2013.

L. Wang, Z. Zhang, W. Rocchia, and E. Alexov. Using DelPhi capabilities to mimic protein’s conformational reorganization with amino acid specific dielectric constants. Communications in computational physics, NIH Public Access, volume 13, issue 1, pages 13, 2013.

C. Li, L. Li, M. Petukh, and E. Alexov. Progress in developing Poisson-Boltzmann equation solvers. Computational and Mathematical Biophysics, De Gruyter, volume 1, issue 1, pages 42-62, 2013.

Z. Zhang, J. Norris, V. Kalscheuer, T. Wood, L. Wang, C. Schwartz, E. Alexov, and H. V. Esch. A Y328C missense mutation in spermine synthase causes a mild form of Snyder--Robinson syndrome. Human molecular genetics, Oxford University Press, volume 22, issue 18, pages 3789-3797, 2013.

M. Petukh, S. Stefl, and E. Alexov. The role of protonation states in ligand-receptor recognition and binding. Current pharmaceutical design, Bentham Science Publishers, volume 19, issue 23, pages 4182-4190, 2013.

S. Decherchi, J. Colmenares, C. E. Catalano, M. Spagnuolo, E. Alexov, and W. Rocchia. Between algorithm and model: different molecular surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution. Communications in computational physics, NIH Public Access, volume 13, pages 61, 2013.

A. V. Onufriev and E. Alexov. Protonation and pK changes in protein-ligand binding. Quarterly reviews of biophysics, NIH Public Access, volume 46, issue 2, pages 181, 2013.

H. Nishi, M. Tyagi, S. Teng, B. A. Shoemaker, K. Hashimoto, E. Alexov, S. Wuchty, and A. R. Panchenko. Cancer missense mutations alter binding properties of proteins and their interaction networks. PloS one, Public Library of Science, volume 8, issue 6, pages e66273, 2013.

S. Stefl, H. Nishi, M. Petukh, A. R. Panchenko, and E. Alexov. Molecular mechanisms of disease-causing missense mutations. Journal of molecular biology, Academic Press, volume 425, issue 21, pages 3919-3936, 2013.

L. Li, C. Li, Z. Zhang, and E. Alexov. On the dielectric “constant” of proteins: smooth dielectric function for macromolecular modeling and its implementation in DelPhi. Journal of chemical theory and computation, American Chemical Society, volume 9, issue 4, pages 2126-2136, 2013.

C. Li, L. Li, and E. Alexov. Parallelized DelPhi: A multiprocessor Poisson-Boltzmann solver to calculate electrostatic energies of biological macromolecules. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 244, 2012.

M. R. GUNNER and E. ALEXOV. CALCULATION OF ELECTROSTATIC FORCES. Molecular Modeling and Dynamics of Bioinorganic Systems, Springer Science \& Business Media, volume 41, pages 361, 2012.

C. Li, M. Zhenirovskyy, L. Li, and E. Alexov. New Parallelized DelPhi: Fast and Efficient Poisson-Boltzmann Solver to Calculate Electrostatics of Large Supramolecular Structures. Biophysical Journal, Elsevier, volume 102, issue 3, pages 270a, 2012.

S. Witham and E. Alexov. Modeling CLIC2-RyR Interactions and the Effect of Disease Causing Mutation. Biophysical Journal, Elsevier, volume 102, issue 3, pages 456a, 2012.

L. Li, L. Wang, C. Li, and E. Alexov. Effect of non-uniform protein dielectric constant on the electrostatic energy calculations. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 244, 2012.

N. Smith, B. Campbell, L. Li, C. Li, and E. Alexov. Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling. BMC structural biology, BioMed Central, volume 12, issue 1, pages 1-10, 2012.

M. Petukh, M. Zhenirovskyy, C. Li, L. Li, L. Wang, and E. Alexov. Predicting nonspecific ion binding using DelPhi. Biophysical journal, Elsevier, volume 102, issue 12, pages 2885-2893, 2012.

C. Li, L. Li, J. Zhang, and E. Alexov. Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi. Journal of computational chemistry, Wiley Online Library, volume 33, issue 24, pages 1960-1966, 2012.

N. Smith, S. Witham, S. Sarkar, J. Zhang, L. Li, C. Li, and E. Alexov. DelPhi web server v2: incorporating atomic-style geometrical figures into the computational protocol. Bioinformatics, Oxford University Press, volume 28, issue 12, pages 1655-1657, 2012.

Z. Zhang, L. Wang, Y. Gao, J. Zhang, M. Zhenirovskyy, and E. Alexov. Predicting folding free energy changes upon single point mutations. Bioinformatics, Oxford University Press, volume 28, issue 5, pages 664-671, 2012.

K. Takano, D. Liu, P. Tarpey, E. Gallant, A. Lam, S. Witham, E. Alexov, A. Chaubey, R. E. Stevenson, C. E. Schwartz, and others. An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity. Human molecular genetics, Oxford University Press, volume 21, issue 20, pages 4497-4507, 2012.

Z. Zhang, M. A. Miteva, L. Wang, and E. Alexov. Analyzing effects of naturally occurring missense mutations. Computational and mathematical methods in medicine, Hindawi, volume 2012, 2012.

L. Li, C. Li, S. Sarkar, J. Zhang, S. Witham, Z. Zhang, L. Wang, N. Smith, M. Petukh, and E. Alexov. DelPhi: a comprehensive suite for DelPhi software and associated resources. BMC biophysics, BioMed Central, volume 5, issue 1, pages 1-11, 2012.

Z. Zhang, J. Norris, C. Schwartz, and E. Alexov. In Silico and In Vitro Investigations of the Mutability of Disease-Causing Missense Mutation Sites in. 2011.

Z. Zhang, C. Schwatz, and E. Alexov. In silico investigation of molecular effects caused by missense mutations in creatine transporter protein. APS March Meeting Abstracts, volume 2011, pages T39-002, 2011.

L. Wang, S. Sarhar, W. Rocchia, and E. Alexov. Using DelPhi capabilities to mimic conformational reorganization with amino acid specific dielectric constants. APS March Meeting Abstracts, volume 2011, pages S1-156, 2011.

Z. Zhang, C. Schwartz, and E. Alexov. In Silico Investigation of Mutability of Spermine Synthase. Biophysical Journal, Elsevier, volume 100, issue 3, pages 321a, 2011.

Z. Zhang, C. Schwatz, and E. Alexov. $\backslash$textit $\{$In silico$\}$ investigation of molecular effects caused by missense mutations in creatine transporter protein. Bulletin of the American Physical Society, American Physical Society, volume 56, 2011.

S. Witham, K. Takano, C. Schwartz, and E. Alexov. In Silico Investigation of a Missense Mutation in CLIC2 Associated with Intellectual Disability. Biophysical Journal, Elsevier, volume 100, issue 3, pages 611a, 2011.

S. Witham, B. Boylen, B. Owesen, W. Rocchia, and E. Alexov. DelPhi webserver: Comprehensive suite for electrostatic calculations of biological macromolecules and their complexes. APS March Meeting Abstracts, volume 2011, pages S1-155, 2011.

S. Witham, K. Talley, L. Wang, Z. Zhang, S. Sarkar, D. Gao, W. Yang, and E. Alexov. Developing hybrid approaches to predict pKa values of ionizable groups. Proteins: Structure, Function, and Bioinformatics, Wiley Subscription Services, Inc., A Wiley Company Hoboken, volume 79, issue 12, pages 3389-3399, 2011.

S. Witham, K. Takano, C. Schwartz, and E. Alexov. A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics. Proteins: Structure, Function, and Bioinformatics, Wiley Subscription Services, Inc., A Wiley Company Hoboken, volume 79, issue 8, pages 2444-2454, 2011.

R. C. Mitra, Z. Zhang, and E. Alexov. In silico modeling of pH-optimum of protein--protein binding. Proteins: Structure, Function, and Bioinformatics, Wiley Subscription Services, Inc., A Wiley Company Hoboken, volume 79, issue 3, pages 925-936, 2011.

Z. Zhang, J. Norris, C. Schwartz, and E. Alexov. In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in spermine synthase. PloS one, Public Library of Science, volume 6, issue 5, pages e20373, 2011.

Z. Zhang, S. Witham, and E. Alexov. On the role of electrostatics in protein--protein interactions. Physical biology, IOP Publishing, volume 8, issue 3, pages 035001, 2011.

E. Alexov, E. L. Mehler, N. Baker, A. M. Baptista, Y. Huang, F. Milletti, J. E. Nielsen, D. Farrell, T. Carstensen, M. H. Olsson, and others. Progress in the prediction of pKa values in proteins. Proteins: structure, function, and bioinformatics, Wiley Subscription Services, Inc., A Wiley Company Hoboken, volume 79, issue 12, pages 3260-3275, 2011.

Z. Zhe, T. Shaolei, and E. Alexov. From 2010 Abstracts Issue. Biophysical Journal, volume 98, pages 1096-1098, 2010.

E. Alexov and B. Honig. Structural and Energetic Basis of Molecular Recognition. Handbook of Cell Signaling, Academic Press, pages 11-13, 2010.

A. Pittman, R. Saul, A. Chaubey, E. Alexov, M. Tiemeyer, R. Steet, C. Schwartz, M. B\'en\'eteau, J. Ricci, V. Desquiret-Dumas, and others. PMCID: PMC2695060. Int Immunol, volume 22, issue 7, pages 593-603, 2010.

Z. Zhe, T. Shaolei, and E. Alexov. In Silico Investigation of the Molecular Effects Caused by Missense Mutations in Spermine Sythase Gene Associated with Human Mental Retardation. Biophysical Journal, Elsevier, volume 98, issue 3, pages 571a, 2010.

S. Teng, A. K. Srivastava, C. E. Schwartz, E. Alexov, and L. Wang. Structural assessment of the effects of Amino Acid Substitutions on protein stability and protein? protein interaction. International journal of computational biology and drug design, Inderscience Publishers, volume 3, issue 4, pages 334-349, 2010.

K. Talley and E. Alexov. On the pH-optimum of activity and stability of proteins. Proteins: Structure, Function, and Bioinformatics, Wiley Subscription Services, Inc., A Wiley Company Hoboken, volume 78, issue 12, pages 2699-2706, 2010.

Z. Zhang, S. Teng, L. Wang, C. E. Schwartz, and E. Alexov. Computational analysis of missense mutations causing Snyder-Robinson syndrome. Human mutation, Wiley Subscription Services, Inc., A Wiley Company Hoboken, volume 31, issue 9, pages 1043-1049, 2010.

R. Mitra, R. Shyam, and E. Alexov. Modeling Ionization Events iduced by Protein Protein Binding. APS Southeastern Section Meeting Abstracts, volume 76, pages PC-003, 2009.

I. Mitra and E. Alexov. Multivariate Analysis of Conformational Changes Induced by Macromolecular Interactions. APS Southeastern Section Meeting Abstracts, volume 76, pages PC-004, 2009.

S. Teng, T. Madej, A. Panchenko, and E. Alexov. Modeling effects of human single nucleotide polymorphisms on protein-protein interactions.(vol 96, pg 2178, 2009). BIOPHYSICAL JOURNAL, CELL PRESS 600 TECHNOLOGY SQUARE, 5TH FLOOR, CAMBRIDGE, MA 02139 USA, volume 96, issue 11, pages 4753-4753, 2009.

R. Shyam and E. Alexov. Accessing the limits of ab initio docking methods. APS Southeastern Section Meeting Abstracts, volume 76, pages PC-002, 2009.

Z. Zhang, S. Teng, and E. Alexov. Computational Modeling of Molecular Effects of Mutations Causing Snyder-Robinson Syndrome. APS Southeastern Section Meeting Abstracts, volume 76, pages PC-007, 2009.

S. Teng, T. Madej, A. Panchenko, and E. Alexov. Modeling effects of human single nucleotide polymorphisms on protein-protein interactions. Biophysical journal, Elsevier, volume 96, issue 6, pages 2178-2188, 2009.

E. Alexov. Editorial [Protein-Protein Interactions Guest Editor: Emil Alexov]. Current pharmaceutical biotechnology, Bentham Science Publishers, volume 9, issue 2, pages 55-56, 2008.

K. Talley, P. Kundrotas, and E. Alexov. Modeling salt dependence of protein-protein association: Linear vs non-linear Poisson-Boltzmann equation. Commun Comput Phys, volume 3, issue 5, pages 1071-1086, 2008.

R. Mitra, R. Shyam, I. Mitra, M. A. Miteva, and E. Alexov. Calculating the protonation states of proteins and small molecules: Implications to ligand-receptor interactions. Current computer-aided drug design, Bentham Science Publishers, volume 4, issue 3, pages 169-179, 2008.

M. Kosloff, E. Alexov, V. Y. Arshavsky, and B. Honig. Electrostatic and lipid anchor contributions to the interaction of transducin with membranes: mechanistic implications for activation and translocation. Journal of Biological Chemistry, Elsevier, volume 283, issue 45, pages 31197-31207, 2008.

K. Talley, C. Ng, M. Shoppell, P. Kundrotas, and E. Alexov. On the electrostatic component of protein-protein binding free energy. PMC biophysics, BioMed Central, volume 1, issue 1, pages 1-23, 2008.

P. J. Kundrotas, M. F. Lensink, and E. Alexov. Homology-based modeling of 3D structures of protein--protein complexes using alignments of modified sequence profiles. International journal of biological macromolecules, Elsevier, volume 43, issue 2, pages 198-208, 2008.

S. Teng, E. Michonova-Alexova, and E. Alexov. Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions. Current pharmaceutical biotechnology, Bentham Science Publishers, volume 9, issue 2, pages 123-133, 2008.

E. Alexov, K. Brock, and P. Kundrotas. Optimization of the electrostatic interactions in protein-protein complexes. APS March Meeting Abstracts, pages K1-021, 2007.

E. G. Alexov. Modeling protein-protein interactions with continuum electrostatics. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 233, pages 52-52, 2007.

P. Kundrotas and E. Alexov. Utilizing Profile-to-Profile Alignments for Predicting Protein-Protein Interactions. APS March Meeting Abstracts, pages K1-020, 2007.

P. Kundrotas and E. Alexov. Predicting protein-protein interactions using non-gapped interacting residue segments. BIOPHYSICAL JOURNAL, pages 367A-368A, 2007.

P. Kundrotas, P. Georgieva, A. Shosheva, P. Christova, and E. Alexov. BANMOKI: A searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families. International journal of biological macromolecules, Elsevier, volume 41, issue 1, pages 114-119, 2007.

M. A. Miteva, E. Alexov, and B. O. Villoutreix. Protein Structure Analysis Online. Current protocols in protein science, volume 50, issue 1, pages 2-13, 2007.

P. Kundrotas and E. Alexov. Predicting interacting and interfacial residues using continuous sequence segments. International journal of biological macromolecules, Elsevier, volume 41, issue 5, pages 615-623, 2007.

P. Kundrotas, P. Georgieva, A. Shosheva, P. Christova, and E. Alexov. Assessing the quality of the homology-modeled 3D structures from electrostatic standpoint: test on bacterial nucleoside monophosphate kinase families. Journal of bioinformatics and computational biology, World Scientific, volume 5, issue 3, pages 693-715, 2007.

A. Isvoran, C. Craescu, and E. Alexov. Electrostatic control of the overall shape of calmodulin: numerical calculations. European Biophysics Journal, Springer-Verlag, volume 36, issue 3, pages 225-237, 2007.

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

K. Brock, K. Talley, K. Coley, P. Kundrotas, and E. Alexov. Optimization of electrostatic interactions in protein-protein complexes. Biophysical journal, Elsevier, volume 93, issue 10, pages 3340-3352, 2007.

P. J. Kundrotas and E. Alexov. PROTCOM: searchable database of protein complexes enhanced with domain--domain structures. Nucleic Acids Research, Oxford University Press, volume 35, issue 1, pages D575-D579, 2007.

C. Bertonati, B. Honig, and E. Alexov. Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophysical journal, Elsevier, volume 92, issue 6, pages 1891-1899, 2007.

C. L. Tang, E. Alexov, A. M. Pyle, and B. Honig. Calculation of pKas in RNA: on the structural origins and functional roles of protonated nucleotides. Journal of molecular biology, Academic Press, volume 366, issue 5, pages 1475-1496, 2007.

P. Kundrotas and E. Alexov. Optimum pH for protein-protein complexes. APS March Meeting Abstracts, pages C1-121, 2006.

E. Alexov, A. Allardice, and P. Kundrotas. Combining biophysical and bioinformatical approaches for predicting residue's contacts. APS March Meeting Abstracts, pages A26-014, 2006.

P. Kundrotas and E. Alexov. Predicting 3D structures of transient protein-protein complexes. APS March Meeting Abstracts, pages A26-007, 2006.

P. J. Kundrotas and E. Alexov. Predicting 3D structures of transient protein--protein complexes by homology. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, Elsevier, volume 1764, issue 9, pages 1498-1511, 2006.

P. J. Kundrotas and E. G. Alexov. Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. BMC bioinformatics, BioMed Central, volume 7, issue 1, pages 1-9, 2006.

P. J. Kundrotas and E. Alexov. Electrostatic properties of protein-protein complexes. Biophysical journal, Elsevier, volume 91, issue 5, pages 1724-1736, 2006.

M. J. Grey, Y. Tang, E. Alexov, C. J. McKnight, D. P. Raleigh, and A. G. Palmer III. 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. Journal of molecular biology, Academic Press, volume 355, issue 5, pages 1078-1094, 2006.

Y. Wu, J. S. Hudson, Q. Lu, J. M. Moore, A. S. Mount, A. M. Rao, E. Alexov, and P. C. Ke. Coating single-walled carbon nanotubes with phospholipids. The Journal of Physical Chemistry B, American Chemical Society, volume 110, issue 6, pages 2475-2478, 2006.

A. Shosheva, A. Donchev, M. Dimitrov, G. Kostov, G. Toromanov, V. Getov, and E. Alexov. Comparative study of the stability of poplar plastocyanin isoforms. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, Elsevier, volume 1748, issue 1, pages 116-127, 2005.

J. Zhu, E. Alexov, and B. Honig. Comparative study of generalized Born models: Born radii and peptide folding. The Journal of Physical Chemistry B, ACS Publications, volume 109, issue 7, pages 3008-3022, 2005.

E. Alexov and M. Gunner. Modeling the First Electron Transfer from QA to QB. Molecular Bioenergetics: Simulations of Electron, Proton, and Energy Transfer, Amer Chemical Society, issue 883, pages 93, 2004.

E. Alexov and M. Gunner. Modeling the First Electron Transfer from QA to QB in Reaction Center Proteins from Rb. sphaeroides. 2004.

C. L. Tang, D. Petrey, M. Fasnacht, M. Kosloff, E. Alexov, and B. Honig. Use of limited suboptimal alignment in homology modeling. Poster presented at 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2004.

A. Shosheva, A. Donchev, M. Dimitrov, I. Zlatanov, G. Toromanov, V. Getov, and E. Alexov. Experimental and numerical study of the poplar plastocyanin isoforms using Tyr as a probe for electrostatic similarity and dissimilarity. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, Elsevier, volume 1698, issue 1, pages 67-75, 2004.

E. Alexov. 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. Proteins: Structure, Function, and Bioinformatics, Wiley Online Library, volume 56, issue 3, pages 572-584, 2004.

E. Alexov. Numerical calculations of the pH of maximal protein stability: The effect of the sequence composition and three-dimensional structure. European Journal of Biochemistry, Blackwell Science Ltd Oxford, UK, volume 271, issue 1, pages 173-185, 2004.

E. Alexov and B. Honig. Proton uptake/release induced by protein-inhibitor association. Application to pepstatin and plasmepsin, cathepsin D and endothiapepsin complexes. BIOPHYSICAL JOURNAL, volume 84, issue 2, pages 505A-505A, 2003.

E. Alexov. Role of the protein side-chain fluctuations on the strength of pair-wise electrostatic interactions: Comparing experimental with computed pKas. Proteins: Structure, Function, and Bioinformatics, Wiley Online Library, volume 50, issue 1, pages 94-103, 2003.

C. L. Tang, L. Xie, I. Y. Koh, S. Posy, E. Alexov, and B. Honig. On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles. Journal of molecular biology, Elsevier, volume 334, issue 5, pages 1043-1062, 2003.

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

C. Tang, E. Alexov, A. Pyle, and B. Honig. Perturbations of pKa in RNA structures: A survey using a Monte Carlo application of the NLPB equation. BIOPHYSICAL JOURNAL, volume 82, issue 1, pages 131A-131A, 2002.

E. Alexov and B. Honig. The origins of pH dependent effects on protein stability: Applications to proteases. Biophysical Journal, volume 82, issue 1, pages 474A-474A, 2002.

J. Tandori, P. Maroti, E. Alexov, P. Sebban, and L. Baciou. Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides. Proceedings of the National Academy of Sciences, National Academy of Sciences, volume 99, issue 10, pages 6702-6706, 2002.

R. E. Georgescu, E. G. Alexov, and M. R. Gunner. Combining conformational flexibility and continuum electrostatics for calculating pKas in proteins. Biophysical journal, Cell Press, volume 83, issue 4, pages 1731-1748, 2002.

W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig. 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. Journal of computational chemistry, Wiley Online Library, volume 23, issue 1, pages 128-137, 2002.

W. Rocchia, E. Alexov, and B. Honig. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions (vol 105B, pg 6507, 2001). Journal of Physical Chemistry B, American Chemical Society (ACS), volume 105, issue 28, pages 6754-6754, 2001.

J. Tandori, L. Baciou, E. Alexov, P. Maroti, M. Schiffer, D. K. Hanson, and P. Sebban. ACCELERATED PUBLICATIONS-Revealing the involvement of extended hydrogen bond networks in the cooperative function between distant sites in bacterial reaction centers. Journal of Biological Chemistry, Baltimore [etc.], volume 276, issue 49, pages 45513-45515, 2001.

W. Rocchia, E. Alexov, and B. Honig. ADDITIONS AND CORRECTIONS-Extending the Applicability of the Nonlinear Poisson-Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions. Journal of Physical Chemistry B-Condensed Phase, Washington, DC: American Chemical Society, c1997-, volume 105, issue 28, pages 6754, 2001.

J. Tandori, L. Baciou, E. Alexov, P. Mar\'oti, M. Schiffer, D. K. Hanson, and P. Sebban. Revealing the involvement of extended hydrogen bond networks in the cooperative function between distant sites in bacterial reaction centers. Journal of Biological Chemistry, Elsevier, volume 276, issue 49, pages 45513-45515, 2001.

W. Rocchia, E. Alexov, and B. Honig. Extending the applicability of the nonlinear Poisson- Boltzmann equation: multiple dielectric constants and multivalent ions. The Journal of Physical Chemistry B, American Chemical Society, volume 105, issue 28, pages 6507-6514, 2001.

E. Alexov, L. Baciou, M. Schiffer, P. Sebban, D. Hanson, and M. Gunner. Modeling the free energy chances due to mutations of residues with multi conformation continuum electrostatic (MCCE) method: Application to reaction center proteins. BIOPHYSICAL JOURNAL, volume 78, issue 1, pages 31A-31A, 2000.

M. Gunner and E. Alexov. Calculating the role of the protein in proton-and electron-transfer reactions. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 219, pages U346-U346, 2000.

M. Gunner and E. Alexov. Reorganization of the QB pocket of photosynthetic reaction centers stabilizes ionization changes. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 220, pages U186-U186, 2000.

M. Gunner, D. Karpman, and E. Alexov. pK (a) calculations with conformational flexibility: the multi conformation continuum electrostatics procedure (MCCE). Biophysical Journal, volume 78, issue 1, pages 31A-31A, 2000.

E. Alexov, J. Miksovska, L. Baciou, M. Schiffer, D. Hanson, P. Sebban, and M. Gunner. Modeling the effects of mutations on the free energy of the first electron transfer from QA-to QB in photosynthetic reaction centers. Biochemistry, ACS Publications, volume 39, issue 20, pages 5940-5952, 2000.

M. Gunner and E. Alexov. A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins. Biochimica et Biophysica Acta (BBA)-Bioenergetics, Elsevier, volume 1458, issue 1, pages 63-87, 2000.

E. Alexov and M. Gunner. Modeling the first electron transfer from QA to QB in reaction centers from the bacteria Rb. Biophysical Journal, volume 76, issue 1, pages A240-A240, 1999.

E. Alexov and M. Gunner. Calculated protein and proton motions coupled to electron transfer: electron transfer from QA-to QB in bacterial photosynthetic reaction centers. Biochemistry, American Chemical Society, volume 38, issue 26, pages 8253-8270, 1999.

M. Gunner and E. Alexov. Modeling motions in protiens that are coupled to electron tranfers. ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, volume 216, pages U159-U159, 1998.

M. Miteva, E. Alexov, and B. Atanasov. Numerical simulation of aldolase tetramer stability. European biophysics journal, Springer-Verlag, volume 28, issue 1, pages 67-73, 1998.

M. R. Gunner and E. Alexov. The Role of the Protein in Modulating Cofactor Electrochemistry in Proteins: The Calculation of Electrostatic Forces. Molecular Modeling and Dynamics of Bioinorganic Systems, Springer, Dordrecht, pages 361-390, 1997.

M. Gunner, E. Alexov, E. Torres, and S. Lipovaca. The importance of the protein in controlling the electrochemistry of heme metalloproteins: methods of calculation and analysis. JBIC Journal of Biological Inorganic Chemistry, Springer-Verlag, volume 2, issue 1, pages 126-134, 1997.

E. Alexov and M. Gunner. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. Biophysical journal, Cell Press, volume 72, issue 5, pages 2075-2093, 1997.

H. Ohshima, E. Mishonova, and E. Alexov. Electrostatic interaction between two charged spherical molecules. Biophysical chemistry, Elsevier, volume 57, issue 23, pages 189-203, 1996.

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

E. Alexov, B. Atanasov, and T. Ueki. Anisotropic behavior of the pH dependence part of Young's modulus in a lysozyme triclinic crystal. Biopolymers: Original Research on Biomolecules, Wiley Subscription Services, Inc., A Wiley Company Hoboken, volume 35, issue 5, pages 513-522, 1995.

E. Alexov. High-Frequency Backward Waves in Longitudinally Magnetized Gyrotropic Waveguides. Contributions to Plasma Physics, WILEY-VCH Verlag Berlin, volume 35, issue 1, pages 23-32, 1995.

E. Alexov and B. Atanasov. Selective absorption of radio frequency energy due to collective motion of charged domains: case of lysozyme crystal. Journal of Biomolecular Structure and Dynamics, Taylor \& Francis Group, volume 13, issue 2, pages 219-228, 1995.

S. Ivanov and E. Alexov. Cherenkov generation of Rayleigh electromagnetic wave in a gyrotropic plasma waveguide. Nuclear Instruments and Methods in Physics Research A, volume 341, issue 1, pages ABS109-ABS110, 1994.

E. Alexov and E. Mishonova. Modeling of the electrostatic potential created by a spherical molecule. Journal of Macromolecular Science, Part B, Taylor \& Francis Group, volume 33, issue 1, pages 21-35, 1994.

E. Alexov and B. Atanasov. Analysis of electrostatic interactions in ribonuclease A monoclinic crystal. Biochimica et Biophysica Acta (BBA)-Protein Structure and Molecular Enzymology, Elsevier, volume 1206, issue 1, pages 55-62, 1994.

E. G. Alexov, S. T. Ivanov, and M. I. Kapchinskii. Rejection band in waveguide filled with cold magnetoactive plasma. Japanese journal of applied physics, IOP Publishing, volume 33, issue 5, pages 2730, 1994.

S. T. Ivanov, K. Ivanova, and E. Alexov. Polaritons along the interface between an anisotropic semiconductor and a metallic screen. Physica Scripta, IOP Publishing, volume 49, issue 2, pages 228, 1994.

S. Ivanov, K. Ivanova, and E. Alexov. Rayleigh surface waves along the boundary between a plasma and a metallic screen. Journal of plasma physics, Cambridge University Press, volume 49, issue 2, pages 227-235, 1993.

E. G. Alexov and S. T. Ivanov. Nonreciprocal effects in a plasma waveguide. IEEE transactions on plasma science, IEEE, volume 21, issue 2, pages 254-257, 1993.

E. Alexov. An additional solution of the waveguide problem for a waveguide partially filled with a magnetoactive semiconductor plasma. Physica Scripta, IOP Publishing, volume 46, issue 5, pages 429, 1992.

E. Alexov and S. Ivanov. Anisotropic TEM-mode in a plasma waveguide. Sov. J. Plasma Phys.(USA), volume 16, pages 283, 1990.

S. Ivanov, E. Alexov, A. Bogdanov, and P. Malinov. Surface wave evolution in a waveguide with an axial plasma column upon changing the external magnetic field. Plasma physics and controlled fusion, IOP Publishing, volume 32, issue 10, pages 791, 1990.

S. Ivanov and E. Alexov. Electromagnetic waves in waveguide partially filled with semiconductor plasma. Contributions to Plasma Physics, WILEY-VCH Verlag Berlin, volume 30, issue 6, pages 763-774, 1990.

S. Ivanov, E. Alexov, and P. Malinov. Waveguide partially filled with semiconductor plasma. Physica Scripta, IOP Publishing, volume 42, issue 4, pages 452, 1990.

S. Ivanov, E. Alexov, and P. Malinov. Nonsymmetrical Electromagnetic Waves in Partially Plasma—Filled Waveguide. Contributions to Plasma Physics, WILEY-VCH Verlag Berlin, volume 30, issue 6, pages 755-762, 1990.

S. Ivanov, A. Bogdanov, and E. Alexov. A new family of electromagnetic waves in a waveguide filled with magnetoactive semiconductor plasma. Physica Scripta, IOP Publishing, volume 42, issue 4, pages 458, 1990.

S. Ivanov and E. Alexov. Electromagnetic waves in a plasma waveguide. Journal of plasma Physics, Cambridge University Press, volume 43, issue 1, pages 51-67, 1990.

S. Ivanov and E. Alexov. Electromagnetic waven in fully-filled plasma waveguide. J. of Plasma, volume 15, pages 1131-1131, 1989.

S. Ivanov and E. Alexov. Electromagnetic waves in the semiconductor plasma waveguide. Physica Scripta, IOP Publishing, volume 40, issue 1, pages 58, 1989.

S. Ivanov, E. Alexov, and P. Malinov. Symmetrical electromagnetic waves in partially-filled plasma waveguide. Plasma physics and controlled fusion, IOP Publishing, volume 31, issue 6, pages 941, 1989.