CosolvKit: a Versatile Tool for Cosolvent MD Preparation and Analysis.

ABSTRACT: Cosolvent molecular dynamics (MDs) are an increasingly popular form of simulations where small molecule cosolvents are added to water-solvated protein systems. These simulations can perform diverse target characterization tasks, including cryptic and allosteric pocket identification and pharmacophore profiling and supplement suites of enhanced sampling methods to explore protein conformational landscapes. The behavior of these systems is tied to the cosolvents used, so the ability to define diverse and complex mixtures is critical in dictating the outcome of the simulations. However, existing methods for preparing cosolvent simulations only support a limited number of predefined cosolvents and concentrations. Here, we present CosolvKit, a tool for the preparation and analysis of systems co

SUBMITTER: Bruciaferri N 

PROVIDER: S-EPMC12810578 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature