Dhiman Ray
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Data-driven enhanced sampling of mechanistic pathways Open
The mechanisms of molecular processes can be characterized by following the minimum free energy pathway (MFEP) on the underlying multidimensional conformational landscapes. Despite recent advancements in enhanced sampling algorithms, obtai…
Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics Open
Noncoding RNAs have recently emerged as promising targets for therapeutic drugs. However, their high conformational flexibility presents significant challenges in structure-based rational drug discovery. Therefore, it is essential to gain …
Enhanced Sampling of Ligand Binding Coupled to RNA Conformational Dynamics Open
As only 1.5 % of the human genome is coded into proteins, noncoding RNAs have emerged in recent days as potential targets of therapeutic drugs. However, due to their high structural flexibility compared to conventional protein targets, it …
Data-driven enhanced sampling of mechanistic pathways Open
The mechanisms of molecular processes can be characterized by following the minimum free energy pathway (MFEP) on the underlying multidimensional conformational landscapes. Despite recent advancements in enhanced sampling algorithms, obtai…
Discriminant Analysis Optimizes Progress Coordinate in Weighted Ensemble Simulations of Rare Event Kinetics Open
Calculating the kinetics of rare-but-important conformational transitions in complex biomolecules is a significant challenge in computational biophysics. Because of the long timescales needed to observe such processes, regular molecular dy…
Data Efficient Learning of Molecular Slow Modes from Nonequilibrium Metadynamics Open
Enhanced sampling simulations help overcome free energy barriers and explore molecular conformational space by applying external bias potential along suitable collective variables (CVs). However, identifying optimal CVs that align with the…
Enhanced Sampling with Sub-optimal Collective Variables: Reconciling Accuracy and Convergence Speed Open
We introduce an enhanced sampling algorithm to obtain converged free energy landscapes of molecular rare events, even when the collective variable (CV) used for biasing is not optimal. Our approach samples a time-dependent target distribut…
Acceleration with Interpretability: Surrogate Model Based Collective Variable for Enhanced Sampling Open
Most enhanced sampling methods facilitate the exploration of molecular free energy landscapes by applying a bias potential along a reduced dimensional collective variable (CV) space. The success of these methods depends on the ability of t…
Discriminant Analysis Optimizes Progress Coordinate in Weighted Ensemble Simulations of Rare Event Kinetics Open
Calculating the kinetics of rare-but-important conformational transitions in complex biomolecules is a significant challenge in computational biophysics. Because of the long timescales needed to observe such processes, regular molecular dy…
A Stochastic Landscape Approach for Protein Folding State Classification Open
Protein folding is a critical process that determines the functional state of proteins. Proper folding is essential for proteins to acquire their functional three-dimensional structures and execute their biological role, whereas misfolded …
A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations Open
The rate constants of enzyme-catalyzed reactions (k_cat) are often approximated from the barrier height of the reactive step. We introduce an enhanced sampling QM/MM approach that directly calculates the kinetics of enzymatic reactions, wi…
Data-driven classification of ligand unbinding pathways Open
Studying the pathways of ligand–receptor binding is essential to understand the mechanism of target recognition by small molecules. The binding free energy and kinetics of protein–ligand complexes can be computed using molecular dynamics (…
A Kinetic View of Enzyme Catalysis from Enhanced Sampling QM/MM Simulations Open
The rate constants of enzyme-catalyzed reactions (k_cat) are often approximated from the barrier height of the reactive step. We introduce an enhanced sampling QM/MM approach that directly calculates the kinetics of enzymatic reactions, wi…
View article: Fluorescence based studies on the interaction and characterization of surface-active ionic liquids with polarity sensitive intramolecular charge transfer probe
Fluorescence based studies on the interaction and characterization of surface-active ionic liquids with polarity sensitive intramolecular charge transfer probe Open
Surface-active ionic liquids (SAILs) are of tremendous interest in recent times due to their improved application in the field of food, detergent, and health. The modulated fluorescence behavior of an intramolecular charge transfer (ICT) p…
Data Driven Classification of Ligand Unbinding Pathways Open
Studying the pathways of ligand-receptor binding is essential to understand the mechanism of target recognition by small molecules. The binding free energy and kinetics of protein-ligand complexes can be computed using molecular dynamics (…
Deep Learning Collective Variables from Transition Path Ensemble Open
The study of the rare transitions that take place between long lived metastable states is a major challenge in molecular dynamics simulations. Many of the methods suggested to address this problem rely on the identification of the slow mod…
A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0] Open
The weighted ensemble (WE) strategy has been demonstrated to be highly efficient in generating pathways and rate constants for rare events such as protein folding and protein binding using atomistic molecular dynamics simulations. Here we …
Unbiased simulation of Alanine Dipeptide in gas phase Open
87 microsecond long unbiased Molecular Dynamics (MD) trajectory of alanine dipeptide in gas phase (traj_comp.xtc). Temperature = 300 K. Force Field: AMBER99SB-ILDN. There are 30+ back and forth transitions between the C_7eq and the C_7ax s…
Unbiased simulation of Alanine Dipeptide in gas phase Open
87 microsecond long unbiased Molecular Dynamics (MD) trajectory of alanine dipeptide in gas phase (traj_comp.xtc). Temperature = 300 K. Force Field: AMBER99SB-ILDN. There are 30+ back and forth transitions between the C_7eq and the C_7ax s…
A Suite of Advanced Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v0.1] Open
We present six advanced tutorials instructing users in the best practices of using key new features and plugins/extensions of the WESTPA 2.0 software package, which consists of major upgrades for enabling applications of the weighted ensem…
Force-Field-Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA Open
The Hoogsteen (HG) base pairing conformation, commonly observed in damaged and mutated DNA helices, facilitates DNA repair and DNA recognition. The free energy difference between HG and Watson-Crick (WC) base pairs has been computed in pre…
Rare Event Kinetics from Adaptive Bias Enhanced Sampling Open
We introduce a novel enhanced sampling approach named OPES flooding for calculating the kinetics of rare events from atomistic molecular dynamics simulation. This method is derived from the On-the-fly-Probability-Enhanced-Sampling (OPES) a…
View article: Simulation of Receptor Binding Domain of SARS-CoV-2 spike protein (WT and variants) in complex with neutralizing antibodies.
Simulation of Receptor Binding Domain of SARS-CoV-2 spike protein (WT and variants) in complex with neutralizing antibodies. Open
This repository contains the molecular dynamics trajectories of the SARS-CoV-2 Spike RBD bound to BD23 and B38 monoclonal antibodies. The simulations for the RBD only systems are also provided. The trajectories are available for the WT spi…
View article: Simulation of Receptor Binding Domain of SARS-CoV-2 spike protein (WT and variants) in complex with neutralizing antibodies.
Simulation of Receptor Binding Domain of SARS-CoV-2 spike protein (WT and variants) in complex with neutralizing antibodies. Open
This repository contains the molecular dynamics trajectories of the SARS-CoV-2 Spike RBD bound to BD23 and B38 monoclonal antibodies. The simulations for the RBD only systems are also provided. The trajectories are available for the WT spi…
Force Field Dependent DNA Breathing Dynamics: A Case Study of Hoogsteen Base Pairing in A6-DNA Open
The Hoogsteen (HG) base pairing (bp) conformation, commonly observed in damaged and mutated DNA helices, facilitates DNA repair and DNA recognition. The free energy difference between HG and Watson-Crick (WC) base pairs has been computed i…
View article: Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies
Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies Open
Mutations in the new variants of SARS-CoV-2 spike protein modulates the dynamics of the neutralizing antibodies. Capturing such modulations from MD simulations and graph network model identifies the role of mutations in facilitating immune…
View article: Simulation of Receptor Binding Domain of SARS-CoV-2 spike protein (WT and variants) in complex with neutralizing antibodies.
Simulation of Receptor Binding Domain of SARS-CoV-2 spike protein (WT and variants) in complex with neutralizing antibodies. Open
This repository contains the molecular dynamics trajectories of the SARS-CoV-2 Spike RBD bound to BD23 and B38 monoclonal antibodies. The simulations for the RBD only systems are also provided. The trajectories are available for the WT spi…
View article: Distant residues modulate conformational opening in SARS-CoV-2 spike protein
Distant residues modulate conformational opening in SARS-CoV-2 spike protein Open
Significance The novel coronavirus (SARS-CoV-2) pandemic resulted in the largest public health crisis in recent times. Significant drug design effort against SARS-CoV-2 is focused on the receptor-binding domain (RBD) of the spike protein, …