COCOMO2: A coarse-grained model for interacting folded and disordered proteins.

ABSTRACT: Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parameterized directly with solubility and phase separation data to improve its performance on predicting concentration-depe

SUBMITTER: Jussupow A 

PROVIDER: S-EPMC11565878 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature