Publications

Publications

You can find all my articles on my Google Scholar profile.

Selected Articles

Topographical Analysis of Electron Density and Electrostatic Potential

Exploring the Gradient Paths and Zero Flux Surfaces of Molecular Electrostatic Potential
Kumar A., Gadre S.R.,
J. Chem. Theory Comput. 2016, 12, 1705–1713.
https://doi.org/10.1021/acs.jctc.6b00073

Lone Pairs: An Electrostatic Viewpoint
Kumar A., Gadre S.R., Mohan N., Suresh C.H.,
J. Phys. Chem. A 2014, 118, 526–532.
https://doi.org/10.1021/jp4117003

Molecular Electrostatics for Probing Lone Pair–π Interactions
Mohan N., Suresh C.H., Kumar A., Gadre S.R.,
Phys. Chem. Chem. Phys. 2013, 15, 18401–18409.
https://doi.org/10.1039/C3CP53379D

Development of DAMQT Package for Topographical Analysis

DAMQT 3: Advanced Suite for the Analysis of Molecular Density and Related Properties in Large Systems
Kumar A., Lopez R., Martinez F., Ramírez G., Ema I., Zorrilla D., Yeole S.D., Gadre S.R.,
Comput. Phys. Commun. 2022, 279, 108460.
https://doi.org/10.1016/j.cpc.2022.108460

DAMQT 2.1.0: A New Version of the DAMQT Package Enabled with the Topographical Analysis of Electron Density and Electrostatic Potential in Molecules
Kumar A., Yeole S.D., Gadre S.R., López R., Rico J.F., Ramírez G., Ema I., Zorrilla D.,
J. Comput. Chem. 2015, 36, 2350–2359.
https://doi.org/10.1002/jcc.24212

Generalization of CHARMM Molecular Force-Field to Small Molecules

Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set
Croitoru A., Kumar A., Lambry J.-C., Lee J., Sharif S., Yu W., MacKerell A.D., Aleksandrov A.,
J. Chem. Theory Comput. 2025, 21(6), 3044–3065.
https://doi.org/10.1021/acs.jctc.5c00046

FFParam-v2.0: A Comprehensive Tool for CHARMM Additive and Drude Polarizable Force-Field Parameter Optimization and Validation
Kumar A., MacKerell A.D.,
J. Phys. Chem. B 2024, 128(18), 4385–4395.
https://doi.org/10.1021/acs.jpcb.4c01314

FFParam: Standalone Package for CHARMM Additive and Drude Polarizable Force Field Parametrization of Small Molecules
Kumar A., Yoluk O., MacKerell A.D.,
J. Comput. Chem. 2020, 41(9), 958–970.
https://doi.org/10.1002/jcc.26138

Development of Drude Polarizable Force Field for Small Molecules

Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Mono-unsaturated Zwitterionic Lipids
Yu Y., Venable R., Thirman J., Chatterjee P., Kumar A., Pastor R., Roux B., MacKerell A.D., Klauda J.,
J. Chem. Theory Comput. 2023, 19(9), 2590–2605.
https://doi.org/10.1021/acs.jctc.3c00203

Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field
Kumar A., Pandey P., Chatterjee P., MacKerell A.D.,
J. Chem. Theory Comput. 2022, 18(3), 1711–1725.
https://doi.org/10.1021/acs.jctc.2c00115

Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field
Chatterjee P., Sengul M., Kumar A., MacKerell A.D.,
J. Chem. Theory Comput. 2022, 18(4), 2388–2407.
https://doi.org/10.1021/acs.jctc.2c00115

Free Energy Estimation Methods

Modeling Ligand Binding Site Water Networks with Site-Identification by Ligand Competitive Saturation: Impact on Ligand Binding Orientations and Relative Binding Affinities
Kumar A., Goel H., Yu W., Zhao M., MacKerell A.D.,
J. Chem. Theory Comput. 2024, 20(24), 11032–11048.
https://doi.org/10.1021/acs.jctc.4c01165

Stereoisomerization of Human Constitutive Androstane Receptor Agonist CITCO
Diethelm-Varela B., Kumar A., Lynch C., Imler G., Deschamps J., Xia M., MacKerell A.D., Xue F.,
Tetrahedron 2021, 79, 131886.
https://doi.org/10.1016/j.tet.2020.131886