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Pradipta Bandyopadhyay - Publications

Affiliations: 
Jawaharlal Nehru University, New Delhi, Delhi, India 
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33 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Srivastava R, Chattopadhyaya M, Bandyopadhyay P. Calculation of salt-dependent free energy of binding of β-lactoglobulin homodimer formation and mechanism of dimer formation using molecular dynamics simulation and three-dimensional reference interaction site model (3D-RISM): diffuse salt ions and non-polar interactions between the monomers favor the dimer formation. Physical Chemistry Chemical Physics : Pccp. PMID 31912070 DOI: 10.1039/C9Cp05578A  0.36
2019 Rakshit A, Bandyopadhyay P, Heindel JP, Xantheas SS. Atlas of putative minima and low-lying energy networks of water clusters n = 3-25. The Journal of Chemical Physics. 151: 214307. PMID 31822087 DOI: 10.1063/1.5128378  0.326
2018 Pandey P, Srivastava R, Bandyopadhyay P. Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test Chemical Physics Letters. 695: 69-78. DOI: 10.1016/J.Cplett.2018.01.059  0.323
2017 Rakshit A, Yamaguchi T, Asada T, Bandyopadhyay P. Understanding the structure and hydrogen bonding network of (H2O)32 and (H2O)33: an improved Monte Carlo temperature basin paving (MCTBP) method and quantum theory of atoms in molecules (QTAIM) analysis Rsc Advances. 7: 18401-18417. DOI: 10.1039/C6Ra28688G  0.3
2016 Asada T, Ando K, Bandyopadhyay P, Koseki S. Free Energy Contribution Analysis Using Response Kernel Approximation: Insights into the Acylation Reaction of a Beta-Lactamase. The Journal of Physical Chemistry. B. PMID 27501066 DOI: 10.1021/Acs.Jpcb.6B06104  0.351
2016 Singh P, Sarkar SK, Bandyopadhyay P. Folding-unfolding transition in the mini-protein villin headpiece (HP35): An equilibrium study using the Wang-Landau algorithm Chemical Physics. 468: 1-8. DOI: 10.1016/J.Chemphys.2016.01.005  0.36
2015 Hasnain S, Bandyopadhyay P. An analytical correlated random walk model and its application to understand subdiffusion in crowded environment. The Journal of Chemical Physics. 143: 114104. PMID 26395684 DOI: 10.1063/1.4930275  0.313
2015 Sharma S, Kumar A, Kundu S, Bandyopadhyay P. Molecular dynamics simulations indicate that TyrosineB10 limits motions of distal Histidine to regulate CO binding in soybean leghemoglobin. Proteins. PMID 26211916 DOI: 10.1002/Prot.24867  0.314
2014 Sahu N, Gadre SR, Rakshit A, Bandyopadhyay P, Miliordos E, Xantheas SS. Low energy isomers of (H2O)25 from a hierarchical method based on Monte Carlo temperature basin paving and molecular tailoring approaches benchmarked by MP2 calculations. The Journal of Chemical Physics. 141: 164304. PMID 25362296 DOI: 10.1063/1.4897535  0.332
2014 Singh P, Sarkar SK, Bandyopadhyay P. Wang-Landau density of states based study of the folding-unfolding transition in the mini-protein Trp-cage (TC5b). The Journal of Chemical Physics. 141: 015103. PMID 25005309 DOI: 10.1063/1.4885726  0.357
2013 Iwata S, Bandyopadhyay P, Xantheas SS. Cooperative roles of charge transfer and dispersion terms in hydrogen-bonded networks of (H2O)n, n = 6, 11, and 16. The Journal of Physical Chemistry. A. 117: 6641-51. PMID 23805893 DOI: 10.1021/Jp403837Z  0.467
2013 Bandyopadhyay P. Increasing the efficiency of Monte Carlo simulation with sampling from an approximate potential Chemical Physics Letters. 556: 341-345. DOI: 10.1016/J.Cplett.2012.11.047  0.309
2013 Rakshit A, Bandyopadhyay P. Finding low energy minima of (H2O)25 and (H2O)30 with temperature basin paving Monte Carlo method with effective fragment potential: New 'global minimum' and graph theoretical characterization of low energy structures Computational and Theoretical Chemistry. 1021: 206-214. DOI: 10.1016/J.Comptc.2013.07.023  0.324
2012 Furtado JP, Rahalkar AP, Shanker S, Bandyopadhyay P, Gadre SR. Facilitating Minima Search for Large Water Clusters at the MP2 Level via Molecular Tailoring. The Journal of Physical Chemistry Letters. 3: 2253-8. PMID 26295779 DOI: 10.1021/Jz300663U  0.345
2012 Shanker S, Bandyopadhyay P. Determination of low-energy structures of a small RNA hairpin using Monte Carlo-based techniques. Journal of Biosciences. 37: 533-8. PMID 22750989 DOI: 10.1007/S12038-012-9209-3  0.312
2012 Sharma S, Bandyopadhyay P. Investigation of the acylation mechanism of class C beta-lactamase: pKa calculation, molecular dynamics simulation and quantum mechanical calculation. Journal of Molecular Modeling. 18: 481-92. PMID 21541744 DOI: 10.1007/S00894-011-1087-3  0.337
2011 Shanker S, Bandyopadhyay P. Monte Carlo temperature basin paving with effective fragment potential: an efficient and fast method for finding low-energy structures of water clusters (H2O)20 and (H2O)25. The Journal of Physical Chemistry. A. 115: 11866-75. PMID 21928813 DOI: 10.1021/Jp2073864  0.35
2011 Singh P, Sarkar SK, Bandyopadhyay P. Understanding the applicability and limitations of Wang–Landau method for biomolecules: Met-enkephalin and Trp-cage Chemical Physics Letters. 514: 357-361. DOI: 10.1016/J.Cplett.2011.08.053  0.318
2009 Bandyopadhyay P, Kuntz ID. Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction. Biopolymers. 91: 68-77. PMID 18781627 DOI: 10.1002/Bip.21083  0.589
2009 Meher BR, Satish Kumar MV, Bandyopadhyay P. Molecular dynamics simulation of HIV-protease with polarizable and non-polarizable force fields Indian Journal of Physics. 83: 81-90. DOI: 10.1007/S12648-009-0005-3  0.331
2008 Bandyopadhyay P. Two-surface Monte Carlo with basin hopping: quantum mechanical trajectory and multiple stationary points of water cluster. The Journal of Chemical Physics. 128: 134103. PMID 18397049 DOI: 10.1063/1.2899020  0.32
2008 Guo X, Bandyopadhyay P, Schilling B, Young MM, Fujii N, Aynechi T, Guy RK, Kuntz ID, Gibson BW. Partial acetylation of lysine residues improves intraprotein cross-linking. Analytical Chemistry. 80: 951-60. PMID 18201069 DOI: 10.1021/Ac701636W  0.63
2007 Bandyopadhyay P. Assessment of Two Surface Monte Carlo (TSMC) method to find stationary points of (H2O)15 and (H2O)20 clusters Theoretical Chemistry Accounts. 120: 307-312. DOI: 10.1007/S00214-007-0300-Z  0.354
2005 Bandyopadhyay P. Accelerating quantum mechanical/molecular mechanical sampling using pure molecular mechanical potential as an importance function: the case of effective fragment potential. The Journal of Chemical Physics. 122: 091102. PMID 15836102 DOI: 10.1063/1.1861890  0.31
2004 Koshkin A, Zhou XT, Kraus CN, Brenner JM, Bandyopadhyay P, Kuntz ID, Barry CE, Ortiz de Montellano PR. Inhibition of Mycobacterium tuberculosis AhpD, an element of the peroxiredoxin defense against oxidative stress. Antimicrobial Agents and Chemotherapy. 48: 2424-30. PMID 15215090 DOI: 10.1128/Aac.48.7.2424-2430.2004  0.486
2003 Chong LT, Bandyopadhyay P, Scanlan TS, Kuntz ID, Kollman PA. Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. Journal of Computational Chemistry. 24: 1371-7. PMID 12868101 DOI: 10.1002/Jcc.10293  0.68
2002 Bandyopadhyay P, Gordon MS, Mennucci B, Tomasi J. An integrated effective fragment-polarizable continuum approach to solvation: Theory and application to glycine Journal of Chemical Physics. 116: 5023-5032. DOI: 10.1063/1.1433503  0.495
2001 Showalter BM, Datta A, Chowdhury PK, Park J, Bandyopadhyay P, Choudhury PK, Kesavan S, Zeng Y, Kraus GA, Gordon MS, Toscano JP, Petrich JW. Identification of a vibrational frequency corresponding to H-atom translocation in hypericin. Photochemistry and Photobiology. 74: 157-63. PMID 11547549 DOI: 10.1562/0031-8655(2001)074<0157:Ioavfc>2.0.Co;2  0.418
2001 Datta A, Bandyopadhyay P, Wen J, Petrich JW, Gordon MS. Coupling of large-amplitude side chain motions to the excited-state H-atom transfer of perylene quinones: Application of theory and experiment to calphostin C Journal of Physical Chemistry A. 105: 1057-1060. DOI: 10.1021/Jp0035941  0.46
2001 Gordon MS, Freitag MA, Bandyopadhyay P, Jensen JH, Kairys V, Stevens WJ. The Effective Fragment Potential Method:  A QM-Based MM Approach to Modeling Environmental Effects in Chemistry The Journal of Physical Chemistry A. 105: 293-307. DOI: 10.1021/Jp002747H  0.486
2000 Bandyopadhyay P, Gordon MS. A combined discrete/continuum solvation model: Application to glycine The Journal of Chemical Physics. 113: 1104-1109. DOI: 10.1063/1.481889  0.456
1999 BANDYOPADHYAY P, TEN-NO S, IWATA S. Ab initioMonte Carlo simulation using multicanonical algorithm: temperature dependence of the average structure of water dimer Molecular Physics. 96: 349-358. DOI: 10.1080/00268979909482968  0.485
1999 Bandyopadhyay P, Ten-no S, Iwata S. Structures and Photoelectron Spectroscopies of Si2C2-Studied with ab Initio Multicanonical Monte Carlo Simulation The Journal of Physical Chemistry A. 103: 6442-6447. DOI: 10.1021/Jp991004X  0.473
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