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Pradipta Bandyopadhyay
Pradipta Bandyopadhyay
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The effective fragment potential method: A QM-based MM approach to modeling environmental effects in chemistry
MS Gordon, MA Freitag, P Bandyopadhyay, JH Jensen, V Kairys, ...
The Journal of Physical Chemistry A 105 (2), 293-307, 2001
7252001
An integrated effective fragment—polarizable continuum approach to solvation: Theory and application to glycine
P Bandyopadhyay, MS Gordon, B Mennucci, J Tomasi
The Journal of chemical physics 116 (12), 5023-5032, 2002
1482002
A combined discrete/continuum solvation model: application to glycine
P Bandyopadhyay, MS Gordon
The Journal of Chemical Physics 113 (3), 1104-1109, 2000
1432000
Facilitating minima search for large water clusters at the MP2 level via molecular tailoring
JP Furtado, AP Rahalkar, S Shanker, P Bandyopadhyay, SR Gadre
The Journal of Physical Chemistry Letters 3 (16), 2253-2258, 2012
792012
Atlas of putative minima and low-lying energy networks of water clusters n= 3–25
A Rakshit, P Bandyopadhyay, JP Heindel, SS Xantheas
The Journal of chemical physics 151 (21), 2019
522019
Partial acetylation of lysine residues improves intraprotein cross-linking
X Guo, P Bandyopadhyay, B Schilling, MM Young, N Fujii, T Aynechi, ...
Analytical chemistry 80 (4), 951-960, 2008
482008
A new coarse-grained model for E. coli cytoplasm: accurate calculation of the diffusion coefficient of proteins and observation of anomalous diffusion
S Hasnain, CL McClendon, MT Hsu, MP Jacobson, P Bandyopadhyay
PLoS One 9 (9), e106466, 2014
462014
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
S Shanker, P Bandyopadhyay
The Journal of Physical Chemistry A 115 (42), 11866-11875, 2011
462011
Riboswitch detection using profile hidden Markov models
P Singh, P Bandyopadhyay, S Bhattacharya, A Krishnamachari, ...
BMC bioinformatics 10, 1-13, 2009
432009
Accelerating quantum mechanical/molecular mechanical sampling using pure molecular mechanical potential as an importance function: the case of effective fragment potential
P Bandyopadhyay
The Journal of chemical physics 122 (9), 091102, 2005
422005
Inhibition of Mycobacterium tuberculosis AhpD, an Element of the Peroxiredoxin Defense against Oxidative Stress
A Koshkin, X Zhou, CN Kraus, JM Brenner, P Bandyopadhyay, ID Kuntz, ...
Antimicrobial agents and chemotherapy 48 (7), 2424-2430, 2004
282004
Cooperative Roles of Charge Transfer and Dispersion Terms in Hydrogen-Bonded Networks of (H2O)n, n = 6, 11, and 16
S Iwata, P Bandyopadhyay, SS Xantheas
The Journal of Physical Chemistry A 117 (30), 6641-6651, 2013
262013
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
N Sahu, SR Gadre, A Rakshit, P Bandyopadhyay, E Miliordos, ...
The Journal of chemical physics 141 (16), 2014
252014
Drug Resistance of HIV‐1 Protease against JE‐2147: I47V mutation investigated by molecular dynamics simulation
P Bandyopadhyay, BR Meher
Chemical biology & drug design 67 (2), 155-161, 2006
252006
A look inside the black box: Using graph-theoretical descriptors to interpret a Continuous-Filter Convolutional Neural Network (CF-CNN) trained on the global and local minimum …
JA Bilbrey, JP Heindel, M Schram, P Bandyopadhyay, SS Xantheas, ...
The Journal of Chemical Physics 153 (2), 2020
232020
Iowa State University
MW Schmidt, KK Baldridge, JA Boatz, ST Elbert, MS Gordon, JH Jensen, ...
J. Comp. Chem 14, 1347, 1993
22*1993
Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to …
P Pandey, R Srivastava, P Bandyopadhyay
Chemical Physics Letters 695, 69-78, 2018
202018
Understanding the structure and hydrogen bonding network of (H 2 O) 32 and (H 2 O) 33: An improved Monte Carlo temperature basin paving (MCTBP) method and quantum theory of …
A Rakshit, T Yamaguchi, T Asada, P Bandyopadhyay
RSC Advances 7 (30), 18401-18417, 2017
192017
Jensen JH. Kairys V, Stevens WJ. The effective fragment potential method: a QM-based MM approach to modeling environmental effects in chemistry
MS Gordon, MA Freitag, P Bandyopadhyay
J Phys Chern A 105, 293-307, 2000
182000
Assessment of Two Surface Monte Carlo (TSMC) method to find stationary points of (H2O)15 and (H2O)20 clusters
P Bandyopadhyay
Theoretical Chemistry Accounts 120 (1), 307-312, 2008
162008
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