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 | 646 | 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 | 139 | 2002 |

A combined discrete/continuum solvation model: application to glycine P Bandyopadhyay, MS Gordon The Journal of Chemical Physics 113 (3), 1104-1109, 2000 | 133 | 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 | 59 | 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 | 48 | 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 | 39 | 2011 |

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 | 36 | 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 | 34 | 2014 |

Riboswitch detection using profile hidden Markov models P Singh, P Bandyopadhyay, S Bhattacharya, A Krishnamachari, ... BMC bioinformatics 10 (1), 325, 2009 | 31 | 2009 |

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 | 23 | 2004 |

Cooperative Roles of Charge Transfer and Dispersion Terms in Hydrogen-Bonded Networks of (H_{2}O)_{n}, *n* = 6, 11, and 16S Iwata, P Bandyopadhyay, SS Xantheas The Journal of Physical Chemistry A 117 (30), 6641-6651, 2013 | 21 | 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 | 21 | 2006 |

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 | 18 | 2000 |

Assessment of Two Surface Monte Carlo (TSMC) method to find stationary points of (H_{2}O)_{15} and (H_{2}O)_{20} clustersP Bandyopadhyay Theoretical Chemistry Accounts 120 (1-3), 307-312, 2008 | 15 | 2008 |

Low energy isomers of (H_{2}O)_{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 | 14 | 2014 |

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 | 14 | 2013 |

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 | 14 | 2013 |

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 | 14 | 2003 |

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 | 14 | 2001 |

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 | 13 | 2017 |