Computational Biophysics and Bioinformatics

A. Das, M. Gur, I. Bahar, and B. Roux
A simple coarse-grained model to map the transition pathway between two stable conformations using the anisotropic elastic network model
Biophysical Journal, 104(2), 35a-36a, 2013
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E. Alexov
Electrostatics and polarization effects in biophysical chemistry: In silico, in vitro, and in vivo
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2013
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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, 2013
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L. Li, C. Li, and E. Alexov
Smooth dielectric function for modeling electrostatics in biological macromolecules
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2013
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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, 104(2), 507a, 2013
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K. Vaidyanathan, T. Niranjan, M. May, R. Rose, C. F. Teo, S. Prabakaran, R. Bridger, E. Alexov, et al.
Characterizing a missense mutation in O-GlcNAc transferase that segregates with disease in a family with X-linked Intellectual Disability
GLYCOBIOLOGY, 2013
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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, 2013
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L. Li, C. Li, and E. Alexov
Modeling Proteins and Small Molecules with Inhomogeneous Dielectric Function: Implementation in Delphi
Biophysical Journal, 104(2), 35a, 2013
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E. Alexov and G.-W. Wei
Preface: Special Issue on Modeling Electrostatics in Molecular Biology (MEMB)
Communications in Computational Physics, 13(1), i-v, 2013
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Z. Zhang, A. Pegg, Y. Ikeguchi, and E. Alexov
Enhancing Human Spermine Synthase Activity by Site Directed Mutations
Biophysical Journal, 104(2), 380a, 2013
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M. Petukh, C. Li, and E. Alexov
Predicting non-specifically bound ions: Application to BION webserver and beryllium disease
Biophysical Journal, 104(2), 506a, 2013
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M. Petukh, T. Kimmet, and E. Alexov
BION web server: predicting non-specifically bound surface ions
Bioinformatics, 29(6), 805-806, 2013
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E. Alexov and M. Sternberg
Understanding molecular effects of naturally occurring genetic differences.
Journal of molecular biology, 425(21), 3911-3913, 2013
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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, 34(22), 1949-1960, 2013
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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, 13(1), 207, 2013
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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, 20(4), 643-651, 2013
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Z. Zhang, Y. Zheng, M. Petukh, A. Pegg, Y. Ikeguchi, and E. Alexov
Enhancing human spermine synthase activity by engineered mutations
PLoS Comput Biol, 9(2), e1002924, 2013
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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, 13(1), 269, 2013
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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, 13(1), 13, 2013
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C. Li, L. Li, M. Petukh, and E. Alexov
Progress in developing Poisson-Boltzmann equation solvers
Computational and Mathematical Biophysics, 1(1), 42-62, 2013
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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, 22(18), 3789-3797, 2013
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M. Petukh, S. Stefl, and E. Alexov
The role of protonation states in ligand-receptor recognition and binding
Current pharmaceutical design, 19(23), 4182-4190, 2013
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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, 13, 61, 2013
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A. V. Onufriev and E. Alexov
Protonation and pK changes in protein-ligand binding
Quarterly reviews of biophysics, 46(2), 181, 2013
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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, 8(6), e66273, 2013
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S. Stefl, H. Nishi, M. Petukh, A. R. Panchenko, and E. Alexov
Molecular mechanisms of disease-causing missense mutations
Journal of molecular biology, 425(21), 3919-3936, 2013
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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, 9(4), 2126-2136, 2013
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Computational Biophysics and Bioinformatics

Professor Emil Alexov Group

2013