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Computational Biophysics and Bioinformatics

Professor Emil Alexov Group

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Journal Articles by A. Chakravorty

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, 22(1), 272, 2021
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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, 60(4), 2229-2246, 2020
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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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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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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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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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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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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, 5, 25, 2018
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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, 14(2), 1020-1032, 2018
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L. Li, Z. Jia, Y. Peng, A. Chakravorty, L. Sun, and E. Alexov
DelPhiForce web server: electrostatic forces and energy calculations and visualization
Bioinformatics, 33(22), 3661-3663, 2017
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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, 33(9), 2283-2295, 2017
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L. Li, A. Chakravorty, and E. Alexov
DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding
Journal of computational chemistry, 38(9), 584-593, 2017
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Conference Papers

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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Patents

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