- Determination of low energy structures of a small RNA hairpin using Monte Carlo based techniques
Sudhanshu Shanker and Pradipta Bandyopadhyay, J. Biosciences (In Press)
- Accurate calculation of the Density of states near the ground
state energy of the peptides Met-enkephalin and (Alanine)5 with the
Wang-Landau method: Lessons learned
Priya Singh and Pradipta Bandyopadhyay, J. Atom. Mol. Opt. Phys. (In Press).
- 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
Sudhanshu Shanker and Pradipta Bandyopadhyay,
J. Phys.
Chem. A 2011, 115 (42), pp 11866–11875
- Understanding the applicability and
limitations of Wang–Landau method for biomolecules: Met-enkephalin
and Trp-cage
Priya Singh, Subir K.
Sarkar, Pradipta Bandyopadhyay,
Chem. Phys. Lett. 514, (2011) 357–361.
- Investigation of the acylation
mechanism of class C beta-lactamase: pKa calculation,
Molecular Dynamics simulation and quantum mechanical
calculation
Smriti Sharma and Pradipta
Bandyopadhyay , Journal of Molecular Modeling
Volume 18, Number 2 (2012), 481-492.
-
Monte Carlo Energy Landscape Paving and Basin Paving
simulation of RNA T-loop hairpin.
Pradipta Bandyopadhyay,Hungyo Kharerin,
Chem. Phys. Lett.,
502, 130 (2011).
-
Efficient
conformational sampling by Monte Carlo Basin Paving method:
Distribution of minima on the energy surface of (H2O)20 and
(H2O)50.
Pradipta Bandyopadhyay,
Chem. Phys. Lett., 487, 133 (2010).
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Riboswitch
detection using profile hidden markov model.
Payal Singh, Pradipta Bandyopadhyay, Sudha
Bhattacharya, A Krishnamachari, Supratim Sengupta,
BMC Bioinformatics, 10, 325 (2009)
-
Computational investigation of kinetics of cross-linking
reactions in proteins: importance in structure prediction.
Pradipta Bandyopadhyay*, Irwin D. Kuntz, Biopolymers, 91,
68 (2009).
*Corresponding author
-
Molecular
Dynamics simulation of HIV-protease with polarizable and non-polarizable
force fields.
B. R. Meher, M. V. Satish Kumar,
Pradipta Bandyopadhyay, Indian Journal of Physics, 83, 81 (2009)
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Two surface
Monte Carlo with Basin Hopping: quantum mechanical trajectory
and multiple stationary points of water clusters.
Pradipta
Bandyopadhyay,
J. Chem.
Phys., 128, 134103 (2008).
-
Partial
Acetylation of Lysine Residues Improves Intra-Protein
Cross-linking ,
Xin Gao,
Pradipta
Bandyopadhyay, Birgit Schilling, Malin M. Young , Naoaki Fujii,
Tiba Aynechi, R. Kiplin Guy, Irwin D. Kuntz and Bradford W.
Gibson,
Analytical
Chemistry, 80, 951, 2008
-
Assessment
of Two Surface Monte Carlo method to find stationary points of
(H2O)15 and (H2O)20 clusters.
Pradipta
Bandyopadhyay,
Theoretical
Chemistry Accounts, 120, 307, 2008.
-
Drug
resistance of HIV-1 Protease against JE-2147: I47V mutation
investigated by molecular dynamics simulation
Pradipta Bandyopadhyay*
and B. R.
Meher, Chemical Biology and Drug Design.67, 155, 2006.
-
Accelerating
QM/MM sampling using pure MM potential: the case of effective
fragment potential.
Pradipta Bandyopadhyay,
Journal of
Chemical Physics, 122, 2005 (1st March issue).
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Direct Hydroxide
attack is a plausible mechanism for amidase antibody 43C9
L. T. Chong, P. Bandyopadhyay, T. S. Scanlan, I. D. Kuntz, P. A.
Kollman. 24, 1371, 2003. J. Comp. Chem.
-
An integrated Effective Fragment-Polarizable Continuum approach
to solvation: Theory and Application to Glycine.
P. Bandyopadhyay, M. S. Gordon, B.
Mennucci, J. Tomasi. J. Chem. Phys., 2002, 116, 5023.
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The effective fragment potential method: a QM-based MM approach
to modeling environmental effects in chemistry.
M. S. Gordon, M. Freitag, P.
Bandyopadhyay, J. H. Jensen, V. Kairys and W. J. Stevens. J.
Phys. Chem. A (feature article), 2001, 105, 293-307.
-
A combined discrete continuum solvation model: application to
glycine.
P. Bandyopadhyay and M. S. Gordon J.
Chem. Phys., 2000, 113, 1104.
-
Ab initio Monte Carlo simulation using multicanonical algorithm:
temperature dependence of the average structure of water dimer.
P. Bandyopadhyay, S. Ten-no, S. Iwata.
Molecular Physics, 1999, 96, 349.
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