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Arghya Chakravorty
Arghya Chakravorty
Verified email at umich.edu
Title
Cited by
Cited by
Year
DelPhi suite: new developments and review of functionalities
C Li, Z Jia, A Chakravorty, S Pahari, Y Peng, S Basu, M Koirala, ...
Journal of computational chemistry 40 (28), 2502-2508, 2019
502019
DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding
L Li, A Chakravorty, E Alexov
Journal of computational chemistry 38 (9), 584-593, 2017
492017
DelPhiForce web server: electrostatic forces and energy calculations and visualization
L Li, Z Jia, Y Peng, A Chakravorty, L Sun, E Alexov
Bioinformatics 33 (22), 3661-3663, 2017
442017
Treating ion distribution with G aussian‐based smooth dielectric function in DelPhi
Z Jia, L Li, A Chakravorty, E Alexov
Journal of computational chemistry 38 (22), 1974-1979, 2017
322017
Modeling electrostatic force in protein-protein recognition
HBM Shashikala, A Chakravorty, E Alexov
Frontiers in Molecular Biosciences 6, 94, 2019
292019
Gaussian-based smooth dielectric function: a surface-free approach for modeling macromolecular binding in solvents
A Chakravorty, Z Jia, Y Peng, N Tajielyato, L Wang, E Alexov
Frontiers in molecular biosciences 5, 25, 2018
262018
A new DelPhi feature for modeling electrostatic potential around proteins: Role of bound ions and implications for zeta-potential
A Chakravorty, Z Jia, L Li, E Alexov
Langmuir 33 (9), 2283-2295, 2017
242017
The HRP3 PWWP domain recognizes the minor groove of double-stranded DNA and recruits HRP3 to chromatin
W Tian, P Yan, N Xu, A Chakravorty, R Liefke, Q Xi, Z Wang
Nucleic acids research 47 (10), 5436-5448, 2019
222019
Reproducing the ensemble average polar solvation energy of a protein from a single structure: Gaussian-based smooth dielectric function for macromolecular modeling
A Chakravorty, Z Jia, L Li, S Zhao, E Alexov
Journal of chemical theory and computation 14 (2), 1020-1032, 2018
222018
Electrostatic component of binding energy: interpreting predictions from poisson–boltzmann equation and modeling protocols
A Chakavorty, L Li, E Alexov
Journal of computational chemistry 37 (28), 2495-2507, 2016
222016
Free Gangliosides Can Alter Amyloid-β Aggregation
A Chakravorty, SD McCalpin, BR Sahoo, A Ramamoorthy, CL Brooks III
The Journal of Physical Chemistry Letters 13, 9303-9308, 2022
212022
Entropy of proteins using multiscale cell correlation
A Chakravorty, J Higham, RH Henchman
Journal of Chemical Information and Modeling 60 (11), 5540-5551, 2020
172020
Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge
HS Ali, A Chakravorty, J Kalayan, SP de Visser, RH Henchman
Journal of computer-aided molecular design 35, 911-921, 2021
122021
Capturing the effects of explicit waters in implicit electrostatics modeling: Qualitative justification of Gaussian-based dielectric models in DelPhi
A Chakravorty, S Panday, S Pahari, S Zhao, E Alexov
Journal of chemical information and modeling 60 (4), 2229-2246, 2020
102020
Modeling electrostatics in molecular biology: A tutorial of DelPhi and associated resources [Article v1. 0]
SK Panday, MHB Shashikala, M Koirala, S Pahari, A Chakvorty, Y Peng, ...
Living Journal of Computational Molecular Science 1 (2), 10841-10841, 2019
82019
pyCHARMM: embedding CHARMM functionality in a python framework
J Buckner, X Liu, A Chakravorty, Y Wu, LF Cervantes, TT Lai, CL Brooks III
Journal of Chemical Theory and Computation 19 (12), 3752-3762, 2023
72023
Total free energy analysis of fully hydrated proteins
J Kalayan, A Chakravorty, J Warwicker, RH Henchman
Proteins: Structure, Function, and Bioinformatics 91 (1), 74-90, 2023
52023
BION-2: predicting positions of non-specifically bound ions on protein surface by a Gaussian-based treatment of electrostatics
HBM Shashikala, A Chakravorty, SK Panday, E Alexov
International Journal of Molecular Sciences 22 (1), 272, 2020
52020
A grid‐based algorithm in conjunction with a gaussian‐based model of atoms for describing molecular geometry
A Chakravorty, E Gallicchio, E Alexov
Journal of computational chemistry 40 (12), 1290-1304, 2019
52019
Reproducing ensemble averaged electrostatics with Super-Gaussian-based smooth dielectric function: application to electrostatic component of binding energy of protein complexes
SK Panday, MH Shashikala, A Chakravorty, S Zhao, E Alexov
Communications in Information and Systems 19 (4), 2019
52019
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Articles 1–20