Members: Publications

Publications

Recent Publications

Google Scholar Profile

Role of water in the pressure-induced unfolding of Bovine Pancreatic Trypsin Inhibitor (BPTI) protein: A molecular dynamics study

UC Roy, P Bandyopadhyay - Chemical Physics Letters 841, 141180, 2024.
Prediction of Ca2+ binding site in proteins with a fast and accurate method based on statistical mechanics and analysis of crystal structures

A Basit, D Choudhury, P Bandyopadhyay - bioRxiv, 2024.03. 03.583063, 2024.
Theoretical insights into the binding interaction of Nirmatrelvir with SARS-CoV-2 Mpro mutants (C145A and C145S): MD simulations and binding free-energy calculation to understand drug resistance.

P Purohit, M Panda, JT Muya, P Bandyopadhyay, BR Meher - Journal of Biomolecular Structure and Dynamics, 1-20, 2023.
Nested Monte Carlo simulation of ionic systems with the primitive model using Debye-Hückel (DH) potential as an importance function and optimizing the DH potential with Kullback-Leibler divergence minimization.

R Srivastava, P Bandyopadhyay - Journal of Chemical Sciences 135 (2), 51, 2023.
Correlation between protein conformations and water structure and thermodynamics at high pressure: A molecular dynamics study of the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein.

Umesh C. Roy and P Bandyopadhyay - The Journal of Chemical Physics, 2023.
Crustwater: Modeling Hydrophobic Solvation.

AK Yadav, P Bandyopadhyay, EA Coutsias, KA Dill - The Journal of Physical Chemistry B, 2022.
Tests of a generalized Barker-Henderson perturbation theory for the phase coexistence diagram of an anisotropic potential.

B Kumari, SK Sarkar, P Bandyopadhyay - Chemical Physics 559, 111533, 2022.
Calcium ion binding to the mutants of calmodulin: a structure-based computational predictive model of binding affinity using a charge scaling approach in molecular dynamics simulation.

A Basit, AK Yadav, P Bandyopadhyay - Journal of Chemical Information and Modeling, 2022.
A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2.

P Priya, A Basit, P Bandyopadhyay - Journal of Biomolecular Structure and Dynamics, 2022.
Analytical 2-Dimensional Model of Nonpolar and Ionic Solvation in Water.

AK Yadav, P Bandyopadhyay, T Urbic, KA Dill - The Journal of Physical Chemistry B, 2021.
Calcium ion binding to calmodulin: binding free energy calculation using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method by incorporating implicit polarization.

A Basit, RK Mishra, P Bandyopadhyay - Journal of Biomolecular Structure and Dynamics, 2021.
Synthetic Tunability and Biophysical Basis for Fabricating Highly Fluorescent and Stable DNA Copper Nanoclusters.

N Tiwari, RK Mishra, S Gupta, R Srivastava… - Langmuir, 2021.
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 energy structures of neutral water clusters.

JA Bilbrey, JP Heindel, M Schram, P Bandyopadhyay… - The Journal of Chemical Physics, 2020.
Calculation of salt-dependent free energy of binding of β-lactoglobulin homodimer formation and mechanism of dimer formation using molecular dynamics simulation and three-dimensional reference interaction site model (3D-RISM): diffuse salt ions and non-polar interactions between the monomers favor the dimer formation.

R Srivastava, M Chattopadhyaya, P Bandyopadhyay - Physical Chemistry Chemical Physics, 2020.
Optimising the parameters of the Gibbs Ensemble Monte Carlo simulation of phase separation: the role of multiple relaxation times.

B Kumari, P Bandyopadhyay, SK Sarkar - Molecular Simulation, 2020.
Atlas of putative minima and low-lying energy networks of water clusters n = 3-25.

A Rakshit, P Bandyopadhyay, JP Heindel… - The Journal of chemical physics, 2019
A comparative evaluation of pair correlation functions for a highly asymmetric electrolyte with mono and divalent counterions from integral equation theory in hypernetted chain (HNC) approximation and Monte Carlo simulation.

P Bandyopadhyay, P Gupta-Bhaya - Chemical Physics Letters, 2019.

Publications topic wise

Calcium Binding Proteins

Solvation Models

DNA-ion Interactions

Synthetic Tunability and Biophysical Basis for Fabricating Highly Fluorescent and Stable DNA Copper Nanoclusters.

N Tiwari, RK Mishra, S Gupta, R Srivastava… - Langmuir, 2021.

Publications

Recent Publications

Google Scholar Profile

Role of water in the pressure-induced unfolding of Bovine Pancreatic Trypsin Inhibitor (BPTI) protein: A molecular dynamics study

Prediction of Ca2+ binding site in proteins with a fast and accurate method based on statistical mechanics and analysis of crystal structures

Theoretical insights into the binding interaction of Nirmatrelvir with SARS-CoV-2 Mpro mutants (C145A and C145S): MD simulations and binding free-energy calculation to understand drug resistance.

Nested Monte Carlo simulation of ionic systems with the primitive model using Debye-Hückel (DH) potential as an importance function and optimizing the DH potential with Kullback-Leibler divergence minimization.

Correlation between protein conformations and water structure and thermodynamics at high pressure: A molecular dynamics study of the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein.

Crustwater: Modeling Hydrophobic Solvation.

Tests of a generalized Barker-Henderson perturbation theory for the phase coexistence diagram of an anisotropic potential.

Calcium ion binding to the mutants of calmodulin: a structure-based computational predictive model of binding affinity using a charge scaling approach in molecular dynamics simulation.

A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2.

Analytical 2-Dimensional Model of Nonpolar and Ionic Solvation in Water.

Calcium ion binding to calmodulin: binding free energy calculation using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method by incorporating implicit polarization.

Synthetic Tunability and Biophysical Basis for Fabricating Highly Fluorescent and Stable DNA Copper Nanoclusters.

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 energy structures of neutral water clusters.

Optimising the parameters of the Gibbs Ensemble Monte Carlo simulation of phase separation: the role of multiple relaxation times.

Atlas of putative minima and low-lying energy networks of water clusters n = 3-25.

A comparative evaluation of pair correlation functions for a highly asymmetric electrolyte with mono and divalent counterions from integral equation theory in hypernetted chain (HNC) approximation and Monte Carlo simulation.

Publications topic wise

Calcium Binding Proteins

Calcium ion binding to the mutants of calmodulin: a structure-based computational predictive model of binding affinity using a charge scaling approach in molecular dynamics simulation.

Calcium ion binding to calmodulin: binding free energy calculation using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method by incorporating implicit polarization.

Solvation Models

Crustwater: Modeling Hydrophobic Solvation.

Analytical 2-Dimensional Model of Nonpolar and Ionic Solvation in Water.

DNA-ion Interactions

Synthetic Tunability and Biophysical Basis for Fabricating Highly Fluorescent and Stable DNA Copper Nanoclusters.

Cytoplasm, molecular crowding, diffusion

Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics.

An analytical correlated random walk model and its application to understand subdiffusion in crowded environment.

A New Coarse-Grained Model for E. coli Cytoplasm: Accurate Calculation of the Diffusion Coefficient of Proteins and Observation of Anomalous Diffusion.

A comparative Brownian dynamics investigation between small linear and circular DNA: Scaling of diffusion coefficient with size and topology of DNA.

Monte Carlo based optimization and water clusters

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 energy structures of neutral water clusters.

Optimising the parameters of the Gibbs Ensemble Monte Carlo simulation of phase separation: the role of multiple relaxation times.

Atlas of putative minima and low-lying energy networks of water clusters n = 3-25.

A comparative evaluation of pair correlation functions for a highly asymmetric electrolyte with mono and divalent counterions from integral equation theory in hypernetted chain (HNC) approximation and Monte Carlo simulation.

Understanding the structure and hydrogen bonding network of (H2O)32 and (H2O)33: an improved Monte Carlo temperature basin paving (MCTBP) method and quantum theory of atoms in molecules (QTAIM) analysis.

A combination of Monte Carlo Temperature Basin Paving and graph theory: water cluster low energy structures and completeness of search.

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.

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 characterization of low energy structures.

Cooperative Roles of Charge Transfer and Dispersion Terms in Hydrogen-Bonded Networks of (H2O)n, n = 6, 11, and 16.

Facilitating Minima Search for Large Water Clusters at MP2 level via Molecular Tailoring.

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.

Efficient conformational sampling by Monte Carlo Basin Paving method: Distribution of minima on the energy surface of (H2O)20 and (H2O)50.

Enhanced sampling and Wang-Landau method

Folding-unfolding transition in the mini-protein villin headpiece (HP35): An equilibrium study using the Wang-Landau algorithm.

Wang-Landau density of states based study of the folding-unfolding transition in the mini-protein Trp-cage (TC5b).

Increasing the efficiency of Monte Carlo simulation with sampling from an approximate potential.

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.

Understanding the applicability and limitations of Wang-Landau method for biomolecules: Met-enkephalin and Trp-cage.

Efficient conformational sampling by Monte Carlo Basin Paving method: Distribution of minima on the energy surface of (H2O)20 and (H2O)50.

Two surface Monte Carlo with Basin Hopping: quantum mechanical trajectory and multiple stationary points of water clusters.

Accelerating QM/MM sampling using pure MM potential: the case of effective fragment potential.

RNA

How Mg2+ ion and water network affect the stability and structure of non-Watson-Crick base pairs in E. coli Loop E of 5S rRNA: A Molecular Dynamics and Reference Interaction Site Model (RISM) study.

Determination of low energy structures of a small RNA hairpin using Monte Carlo based techniques.

Monte Carlo Energy Landscape Paving and Basin Paving simulation of RNA T-loop hairpin.

Application to biological systems

A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2.

Computational approach for molecular design using free energy contribution analysis.

Free Energy Contribution Analysis Using Response Kernel Approximation: Insights into the Acylation Reaction of a Beta-Lactamase.

Molecular dynamics simulations indicate that tyrosineB10 limits motions of distal histidine to regulate CO binding in soybean leghemoglobin.

Inter-chain hydrophobic clustering promotes rigidity in HIV-1 protease flap dynamics: New insights from Molecular Dynamics.

Conformational Dynamics of HIV-1 protease: a comparative molecular dynamics simulation study with multiple amber force fields.

Investigation of the acylation mechanism of class C beta-lactamase: pKa calculation, Molecular Dynamics simulation and quantum mechanical calculation.

Molecular Dynamics simulation of HIV-protease with polarizable and non-polarizable force fields.

Drug resistance of HIV-1 Protease against JE-2147: I47V mutation investigated by molecular dynamics simulation.

Others

Computational approach for molecular design using free energy contribution analysis.

Comparison of molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics-three-dimensional reference interaction site model (MM-3D-RISM) method to calculate the binding free energy of protein-ligand complexes: Effect of metal ion and advance statistical test.

Identification of inhibitors against α-Isopropylmalate Synthase of Mycobacterium tuberculosis using docking-MM/PBSA hybrid approach.

Computational investigation of kinetics of cross-linking reactions in proteins: importance in structure prediction.

Riboswitch detection using profile hidden markov models.

Partial Acetylation of Lysine Residues Improves Intra-Protein Cross-linking.

Selected publications from Ph.D. and Post-doc days

Direct Hydroxide attack is a plausible mechanism for amidase antibody 43C9.

An integrated Effective Fragment-Polarizable Continuum approach to solvation: Theory and Application to Glycine.

The effective fragment potential method: a QM-based MM approach to modeling environmental effects in chemistry.

Understanding the structure and hydrogen bonding network of (H₂O)₃₂ and (H₂O)₃₃: an improved Monte Carlo temperature basin paving (MCTBP) method and quantum theory of atoms in molecules (QTAIM) analysis.

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.

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 characterization of low energy structures.

Cooperative Roles of Charge Transfer and Dispersion Terms in Hydrogen-Bonded Networks of (H₂O)_n, n = 6, 11, and 16.

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.

Efficient conformational sampling by Monte Carlo Basin Paving method: Distribution of minima on the energy surface of (H₂O)₂₀ and (H₂O)₅₀.

Efficient conformational sampling by Monte Carlo Basin Paving method: Distribution of minima on the energy surface of (H₂O)₂₀ and (H₂O)₅₀.

How Mg²⁺ ion and water network affect the stability and structure of non-Watson-Crick base pairs in E. coli Loop E of 5S rRNA: A Molecular Dynamics and Reference Interaction Site Model (RISM) study.