Publications
- Kumar A.,1, Lopez R, Martinez F., Ramırez G., Ema I., Zorrilla D., Yeole S.D., Gadre S.R., DAMQT 3: Advanced suite for the analysis of molecular density and related properties in large systems (Accepted).
- Kumar A., Pandey P., Chatterjee P., MacKerell A.D., Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field, J. Chem. Theory Comput., 2022, 18, 3, 1711–1725.
- Chatterjee, P. Sengul, M. Kumar, A., MacKerell, A.D., Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field, J. Chem. Theory Comput., 2022.
- Croitoru A., Park S., Kumar A., Lee J., Im W., MacKerell, A.D., Aleksandrov A., Additive CHARMM36 Force Field for Nonstandard Amino Acids, J. Chem. Theory Comput. 2021, 17, 6, 3554–3570.
- Srivastava P., Verma M., Kumar A., Srivastava P., Mishra R. Sri S., Patra A.K., Luminescent Naphthalimide-Tagged Ruthenium(II)-Arene Complexes: Cellular Imaging, Photocytotoxicity and Transferrin Binding, Dalton Trans. 2021, 50, 3629-3640.
- Nedyalkova M., Vasighi M., Sappati S., Kumar A., Madurga S., Simeonov V., Inhibition Ability of Natural Compounds on Receptor-Binding Domain of SARS-CoV2: An In Silico Approach, Pharmaceuticals, 2021, 14 (12), 1328.
- Diethelm-Varela B., Kumar A., Lynch C., Imler G., Deschamps J., Xia M., MacKerell Jr. A.D., Xue F. Stereoisomerization of human constitutive androstane receptor agonist CITCO, Tetrahedron 2021, 79, 1318862.
- Kumar A., Yoluk O., MacKerell Jr A.D., FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules, J. Comp. Chem. 2020, 41 (9), 958-970.
- Turchi M., Kognole A.A., Kumar A., Cai Q., Lian G., MacKerell Jr A.D., Predicting Partition Coefficients of Neutral and Charged Solutes in the Mixed SLES–Fatty Acid Micellar System, J. Phys. Chem. B 2020, 124 (9), 1653-1664.
- Kumar A., MacKerell Jr. A.D., Use of Cyano Probes in QM/MM Simulations to Study the Effect of Ion Concentration and Temperature of the Environment on a Uracil Nucleotide and DNA, Biophysical J. 2019, 116 (3), 357a.
- López R., Rico J.F., Ramírez G., Ema I., Zorrilla D., Kumar A., Yeole S.D., Gadre S.R., Topography of Molecular Electron density and electrostatic potential with DAMQT, Comput. Phys. Comm. , 2017, 214, 207‐215.
- Gadre S.R., Kumar A., Bonding and Reactivity Patterns from Electrostatic Landscapes of Molecules, J. Chem. Sci. 2016, 128, 1519–1526.
- Kumar A., Gadre S.R., Molecular Electrostatic Potential based Atoms in Molecules: Shielding Effects and Reactivity Patterns, Aust. J. Chem., 2016, 69, 975‐982.
- Kumar A., Gadre S.R., Exploring the Gradient Paths and Zero Flux Surfaces of Molecular Electrostatic Potential, J. Chem. Theory Comput. 2016, 12, 1705–1713.
- Kumar A., Yeole S.D., Gadre S.R., López R., Rico J.F., Ramírez G., Ema I., Zorrilla D., DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules, J. Comput. Chem. 2015, 36, 2350‐2359.
- Kumar A., Gadre S.R., On the electrostatic nature of electrides, Phys. Chem.Chem. Phys. 2015, 17, 15030‐15035.
- Kumar A., Gadre S.R., Chenxia X., Tianlv X., Kirk S.R., Jenkins S., Hybrid QTAIM and electrostatic potential‐based quantum topology phase diagrams for water clusters, Phys. Chem. Chem. Phys. 2015, 17, 15258‐15273.
- Gadre S.R., Kumar A., Understanding Lone Pair‐π Interactions from Electrostatic Viewpoint in Noncovalent Forces, Ed. S. Scheiner, Springer Switzerland, 2015, 391‐418.
- Kumar A., Gadre S.R., Mohan N., Suresh C.H., Lone Pairs: An Electrostatic Viewpoint, J. Phys. Chem. A. 2014, 118, 526‐532.
- Sarmah S., Guha A.K., Phukan A.K., Kumar A., Gadre S.R., Stabilization of Si (0) and Ge (0) compounds by different silylenes and germylenes: a density functional and molecular electrostatic study, Dalton Trans. 2013, 42, 13200‐13209.
- Mohan N., Suresh C.H., Kumar A., Gadre S.R., Molecular electrostatics for probing lone pair–π interactions, Phys. Chem. Chem. Phys. 2013, 15, 18401‐18409.