Nishita Mandal

This study benchmarks coarse-grained simulation methods for analyzing enzyme transport tunnels, finding they efficiently capture tunnel geometry but vary in replicating all-atom dynamics.

This study uses Gaussian accelerated MD simulations to improve tunnel sampling in enzymes, revealing new transient tunnels and their functional relevance.

TransportTools enables efficient analysis of ligand transport pathways through voids in biomolecules using high-throughput molecular dynamics data.