@article{das2013simple, author = "A. Das and M. Gur and I. Bahar and B. Roux", title = "A simple coarse-grained model to map the transition pathway between two stable conformations using the anisotropic elastic network model", year = 2013, journal = "Biophysical Journal", publisher = "Elsevier", volume = 104, number = 2, pages = "35a-36a" } @inproceedings{alexov2013electrostatics, author = "E. Alexov", title = "Electrostatics and polarization effects in biophysical chemistry: In silico, in vitro, and in vivo", year = 2013, booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY", volume = 246 } @inproceedings{petukh2013electrostatics, author = "M. Petukh and A. Panchenko and E. Alexov", title = "Electrostatics plays significant role in changes of the protein-protein affinity due to missense mutations", year = 2013, booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY", volume = 246 } @inproceedings{li2013smooth, author = "L. Li and C. Li and E. Alexov", title = "Smooth dielectric function for modeling electrostatics in biological macromolecules", year = 2013, booktitle = "ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY", volume = 246 } @article{li2013multi, author = "C. Li and M. Petukh and L. Li and E. Alexov", title = "Multi-Level and Interleaved Poisson-Boltzmann (MLIPB) Method for Parallel Computing of the Electrostatics and its Application in Delphi", year = 2013, journal = "Biophysical Journal", publisher = "Elsevier", volume = 104, number = 2, pages = "507a" } @inproceedings{vaidyanathan2013characterizing, author = "K. Vaidyanathan and T. Niranjan and M. May and R. Rose and C. F. Teo and S. Prabakaran and R. Bridger and E. Alexov and T. Wang and C. Schwartz and others", title = "Characterizing a missense mutation in O-GlcNAc transferase that segregates with disease in a family with X-linked Intellectual Disability", year = 2013, booktitle = "GLYCOBIOLOGY", volume = 23, number = 11, pages = "1334-1335" } @inproceedings{zhang2013snyder, author = "Z. Zhang and V. Martiny and D. Lagorce and E. Alexov and M. Miteva and others", title = "Snyder-Robinson Syndrome: Rescuing the Disease-Causing Effect of G56S mutant by Small Molecule Binding", year = 2013, booktitle = "APS March Meeting Abstracts", volume = 2013, pages = "G45-005" } @article{li2013modeling, author = "L. Li and C. Li and E. Alexov", title = "Modeling Proteins and Small Molecules with Inhomogeneous Dielectric Function: Implementation in Delphi", year = 2013, journal = "Biophysical Journal", publisher = "Elsevier", volume = 104, number = 2, pages = "35a" } @article{alexov2013preface, author = "E. Alexov and G.-W. Wei", title = "Preface: Special Issue on Modeling Electrostatics in Molecular Biology (MEMB)", year = 2013, journal = "Communications in Computational Physics", publisher = "Cambridge University Press", volume = 13, number = 1, pages = "i-v" } @article{zhang2013enhancing, author = "Z. Zhang and A. Pegg and Y. Ikeguchi and E. Alexov", title = "Enhancing Human Spermine Synthase Activity by Site Directed Mutations", year = 2013, journal = "Biophysical Journal", publisher = "Elsevier", volume = 104, number = 2, pages = "380a" } @article{petukh2013predicting, author = "M. Petukh and C. Li and E. Alexov", title = "Predicting non-specifically bound ions: Application to BION webserver and beryllium disease", year = 2013, journal = "Biophysical Journal", publisher = "Elsevier", volume = 104, number = 2, pages = "506a" } @article{petukh2013bion, author = "M. Petukh and T. Kimmet and E. Alexov", title = "BION web server: predicting non-specifically bound surface ions", year = 2013, journal = "Bioinformatics", publisher = "Oxford University Press", volume = 29, number = 6, pages = "805-806" } @article{alexov2013understanding, author = "E. Alexov and M. Sternberg", title = "Understanding molecular effects of naturally occurring genetic differences.", year = 2013, journal = "Journal of molecular biology", volume = 425, number = 21, pages = "3911-3913" } @article{li2013continuous, author = "C. Li and M. Petukh and L. Li and E. Alexov", title = "Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi", year = 2013, journal = "Journal of computational chemistry", publisher = "Wiley Online Library", volume = 34, number = 22, pages = "1949-1960" } @article{wang2013silico, author = "L. Wang and S. Witham and Z. Zhang and L. Li and M. E. Hodsdon and E. Alexov", title = "In silico investigation of pH-dependence of prolactin and human growth hormone binding to human prolactin receptor", year = 2013, journal = "Communications in computational physics", publisher = "NIH Public Access", volume = 13, number = 1, pages = "207" } @article{zhang2013rational, author = "Z. Zhang and S. Witham and M. Petukh and G. Moroy and M. Miteva and Y. Ikeguchi and E. Alexov", title = "A rational free energy-based approach to understanding and targeting disease-causing missense mutations", year = 2013, journal = "Journal of the American Medical Informatics Association", publisher = "BMJ Publishing Group BMA House, Tavistock Square, London, WC1H 9JR", volume = 20, number = 4, pages = "643-651" } @article{zhang2013enhancing, author = "Z. Zhang and Y. Zheng and M. Petukh and A. Pegg and Y. Ikeguchi and E. Alexov", title = "Enhancing human spermine synthase activity by engineered mutations", year = 2013, journal = "PLoS Comput Biol", publisher = "Public Library of Science", volume = 9, number = 2, pages = "e1002924" } @article{sarkar2013delphi, author = "S. Sarkar and S. Witham and J. Zhang and M. Zhenirovskyy and W. Rocchia and E. Alexov", title = "DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes", year = 2013, journal = "Communications in computational physics", publisher = "NIH Public Access", volume = 13, number = 1, pages = "269" } @article{wang2013using, author = "L. Wang and Z. Zhang and W. Rocchia and E. Alexov", title = "Using DelPhi capabilities to mimic protein’s conformational reorganization with amino acid specific dielectric constants", year = 2013, journal = "Communications in computational physics", publisher = "NIH Public Access", volume = 13, number = 1, pages = "13" } @article{li2013progress, author = "C. Li and L. Li and M. Petukh and E. Alexov", title = "Progress in developing Poisson-Boltzmann equation solvers", year = 2013, journal = "Computational and Mathematical Biophysics", publisher = "De Gruyter", volume = 1, number = 1, pages = "42-62" } @article{zhang2013y328c, author = "Z. Zhang and J. Norris and V. Kalscheuer and T. Wood and L. Wang and C. Schwartz and E. Alexov and H. V. Esch", title = "A Y328C missense mutation in spermine synthase causes a mild form of Snyder--Robinson syndrome", year = 2013, journal = "Human molecular genetics", publisher = "Oxford University Press", volume = 22, number = 18, pages = "3789-3797" } @article{petukh2013role, author = "M. Petukh and S. Stefl and E. Alexov", title = "The role of protonation states in ligand-receptor recognition and binding", year = 2013, journal = "Current pharmaceutical design", publisher = "Bentham Science Publishers", volume = 19, number = 23, pages = "4182-4190" } @article{decherchi2013between, author = "S. Decherchi and J. Colmenares and C. E. Catalano and M. Spagnuolo and E. Alexov and W. Rocchia", title = "Between algorithm and model: different molecular surface definitions for the Poisson-Boltzmann based electrostatic characterization of biomolecules in solution", year = 2013, journal = "Communications in computational physics", publisher = "NIH Public Access", volume = 13, pages = "61" } @article{onufriev2013protonation, author = "A. V. Onufriev and E. Alexov", title = "Protonation and pK changes in protein-ligand binding", year = 2013, journal = "Quarterly reviews of biophysics", publisher = "NIH Public Access", volume = 46, number = 2, pages = "181" } @article{nishi2013cancer, author = "H. Nishi and M. Tyagi and S. Teng and B. A. Shoemaker and K. Hashimoto and E. Alexov and S. Wuchty and A. R. Panchenko", title = "Cancer missense mutations alter binding properties of proteins and their interaction networks", year = 2013, journal = "PloS one", publisher = "Public Library of Science", volume = 8, number = 6, pages = "e66273" } @article{stefl2013molecular, author = "S. Stefl and H. Nishi and M. Petukh and A. R. Panchenko and E. Alexov", title = "Molecular mechanisms of disease-causing missense mutations", year = 2013, journal = "Journal of molecular biology", publisher = "Academic Press", volume = 425, number = 21, pages = "3919-3936" } @article{li2013dielectric, author = "L. Li and C. Li and Z. Zhang and E. Alexov", title = "On the dielectric “constant” of proteins: smooth dielectric function for macromolecular modeling and its implementation in DelPhi", year = 2013, journal = "Journal of chemical theory and computation", publisher = "American Chemical Society", volume = 9, number = 4, pages = "2126-2136" }