Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM.

ABSTRACT: Quantifying the conformational ensembles of biomolecules is fundamental to describing mechanisms of processes such as protein folding, interconversion between folded states, ligand binding, and allosteric regulation. Accurate quantification of these ensembles remains a challenge for conventional molecular simulations of all but the simplest molecules due to insufficient sampling. Enhanced sampling approaches, such as metadynamics, were designed to overcome this challenge; however, the nonuniform frame weights that result from many of these approaches present an additional challenge to ensemble quantification techniques such as Markov State Modeling or structural clustering. Here, we present rigorous inclusion of nonuniform frame weights into a structural clustering method entitled shapeGMM

SUBMITTER: Sasmal S 

PROVIDER: S-EPMC11104435 | biostudies-literature | 2024 May

REPOSITORIES: biostudies-literature