|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
|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
|A combined discrete/continuum solvation model: application to glycine|
P Bandyopadhyay, MS Gordon
The Journal of Chemical Physics 113 (3), 1104-1109, 2000
|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
|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
|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
|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 (9), 091102, 2005
|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
|Riboswitch detection using profile hidden Markov models|
P Singh, P Bandyopadhyay, S Bhattacharya, A Krishnamachari, ...
BMC bioinformatics 10 (1), 325, 2009
|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
|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
|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
|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
|Gamess user's guide|
MW Schmidt, KK Baldridge, JA Boatz, ST Elbert, MS Gordon, JJ Jensen, ...
Ames, Iowa: Iowa State University, 2007
|Assessment of Two Surface Monte Carlo (TSMC) method to find stationary points of (H2O)15 and (H2O)20 clusters|
Theoretical Chemistry Accounts 120 (1-3), 307-312, 2008
|Low energy isomers of (H2O)25 from a hierarchical method based on Monte Carlo temperature basin paving and molecular tailoring approaches …|
N Sahu, SR Gadre, A Rakshit, P Bandyopadhyay, E Miliordos, ...
The Journal of chemical physics 141 (16), 164304, 2014
|Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9|
LT Chong, P Bandyopadhyay, TS Scanlan, ID Kuntz, PA Kollman
Journal of computational chemistry 24 (12), 1371-1377, 2003
|Identification of a Vibrational Frequency Corresponding to H‐atom Translocation in Hypericin¶|
BM Showalter, A Datta, PK Chowdhury, J Park, P Bandyopadhyay, ...
Photochemistry and photobiology 74 (2), 157-163, 2001
|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|
A Datta, P Bandyopadhyay, J Wen, JW Petrich, MS Gordon
The Journal of Physical Chemistry A 105 (6), 1057-1060, 2001
|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 …|
A Rakshit, P Bandyopadhyay
Computational and Theoretical Chemistry 1021, 206-214, 2013