Computational Biophysics and Bioinformatics

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, 2019
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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, 2019
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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, 19(4), 2019
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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, 7, e8106, 2019
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S. K. Panday, M. H. Shashikala, M. Koirala, S. Pahari, A. Chakvorty, Y. Peng, L. Li, Z. Jia, et al.
Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]
Living Journal of Computational Molecular Science, 1(2), 10841, 2019
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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, 20(19), 4828, 2019
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H. Shashikala, A. Chakravorty, and E. Alexov
Modeling electrostatic force in protein-protein recognition
Frontiers in molecular biosciences, 6, 94, 2019
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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, 6, 74, 2019
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C. Li, Z. Jia, A. Chakravorty, S. Pahari, Y. Peng, S. Basu, M. Koirala, S. K. Panday, et al.
DelPhi suite: New developments and review of functionalities
Journal of computational chemistry, 40(28), 2502-2508, 2019
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N. Tajielyato and E. Alexov
Modeling pKas of unfolded proteins to probe structural models of unfolded state
Journal of Theoretical and Computational Chemistry, 18(4), 1950020, 2019
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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, 79(2), 631-672, 2019
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C. J. Spellicy, Y. Peng, L. Olewiler, S. S. Cathey, R. C. Rogers, D. Bartholomew, J. Johnson, E. Alexov, et al.
Three additional patients with EED-associated overgrowth: potential mutation hotspots identified?
Journal of human genetics, 64(6), 561-572, 2019
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N. Tajielyato and E. Alexov
Processivity vs. beating: Comparing cytoplasmic and axonemal dynein microtubule binding domain association with microtubule
International journal of molecular sciences, 20(5), 1090, 2019
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S. Pahari, L. Sun, and E. Alexov
PKAD: a database of experimentally measured pKa values of ionizable groups in proteins
Database, 2019, 2019
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M. S. H. Bosthanthirige, A. Chakravorty, and E. Alexov
Modeling Electrostatic Force in Protein-Protein Recognition
Biophysical Journal, 116(3), 46a, 2019
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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, 116(3), 561a-562a, 2019
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N. Tajielyato, J. Alper, and E. Alexov
Comparative Study of Flagellar and Cytoplasmic Dyneins
Biophysical Journal, 116(3), 560a, 2019
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S. Pahari, L. Sun, and E. Alexov
Surface-Free Protocol for Computing PKA's (DelPhiPKa): Applications to Protein-Protein Interactions
Biophysical Journal, 116(3), 166a, 2019
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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, 116(3), 192a, 2019
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Y. Peng, M. Koirala, and E. Alexov
Electrostatic Force Driven Molecular Dynamics Simulations
Biophysical Journal, 116(3), 290a, 2019
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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, 40(12), 1290-1304, 2019
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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, 20(3), 548, 2019
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Computational Biophysics and Bioinformatics

Professor Emil Alexov Group

2019