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 | 50 | 2019 |
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 | 49 | 2017 |
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 | 44 | 2017 |
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 | 32 | 2017 |
Modeling electrostatic force in protein-protein recognition HBM Shashikala, A Chakravorty, E Alexov Frontiers in Molecular Biosciences 6, 94, 2019 | 29 | 2019 |
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 | 26 | 2018 |
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 | 24 | 2017 |
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 | 23 | 2019 |
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 | 22 | 2022 |
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 | 22 | 2018 |
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 | 22 | 2016 |
Entropy of proteins using multiscale cell correlation A Chakravorty, J Higham, RH Henchman Journal of Chemical Information and Modeling 60 (11), 5540-5551, 2020 | 18 | 2020 |
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 | 13 | 2021 |
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 | 10 | 2020 |
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 | 8 | 2019 |
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 | 7 | 2023 |
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 | 5 | 2023 |
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 | 5 | 2020 |
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 | 5 | 2019 |
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 | 5 | 2019 |