84 citations · 202 across the 5 of their papers we have counts for
5 papers
Data Driven Classification of Ligand Unbinding Pathways
Dhiman Ray, Michele Parrinello
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-…
Deep Learning Collective Variables from Transition Path Ensemble
Dhiman Ray, Enrico Trizio, Michele Parrinello
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 addr…
Rare Event Kinetics from Adaptive Bias Enhanced Sampling
Dhiman Ray, Narjes Ansari, Valerio Rizzi +2
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…
Kinetics and Free Energy of Ligand Dissociation Using Weighted Ensemble Milestoning
Dhiman Ray, Trevor Gokey, David L. Mobley +1
We consider the recently developed weighted ensemble milestoning (WEM) scheme [J. Chem. Phys. 152, 234114 (2020)], and test its capability of simulating ligand-receptor dissociatio…
Weighted Ensemble Milestoning (WEM): A Combined Approach for Rare Event Simulations
Dhiman Ray, Ioan Andricioaei
To directly simulate rare events using atomistic molecular dynamics is a significant challenge in computational biophysics. Well-established enhanced-sampling techniques do exist t…