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Pradipta Bandyopadhyay
Pradipta Bandyopadhyay
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Year
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
7312001
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
1492002
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
542019
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
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
252020
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
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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