Computational methods constitute efficient strategies for screening and optimizing potential
drug molecules. A critical factor in this process is the binding affinity between candidate …

Protein dynamics play a crucial role in biological function, encompassing motions ranging
from atomic vibrations to large-scale conformational changes. Recent advancements in …

Alchemical relative binding free energy calculations have recently found important
applications in drug optimization. A series of congeneric compounds are generated from a …

It is increasingly widely recognized that ensemble-based approaches are required to
achieve reliability, accuracy, and precision in molecular dynamics calculations. The purpose …

Uncertainty quantification (UQ) is rapidly becoming a sine qua non for all forms of
computational science out of which actionable outcomes are anticipated. Much of the …

We introduce the lambda-Adaptive Biasing Force (lambda-ABF) method for the computation
of alchemical free-energy differences. We propose a software implementation and …

The COVID-19 pandemic, instigated by the emergence of the novel coronavirus, SARS-CoV-
2, created an incomparable global health crisis. Due to its highly virulent nature, identifying …

Free energy calculations for protein–ligand complexes have become widespread in recent
years owing to several conceptual, methodological and technological advances. Central …

Biomolecular research traditionally revolves around comprehending the mechanisms
through which peptides or proteins facilitate specific functions, often driven by their …

ABSTRACT The Nipah virus (NiV) is an emerging pathogenic paramyxovirus that causes
severe viral infection with a high mortality rate. This study aimed to model the effectual …