Optimized protein-water interactions and torsional refinements yield balanced atomistic protein force fields.

ABSTRACT: All-atom molecular dynamics (MD) simulations based on physics-based force fields serve as an essential complement to experiments for investigating protein structure, dynamics, and interactions. Despite significant advances in force field parameterization, achieving a consistent balance of molecular interactions that stabilize folded proteins while accurately capturing the conformational dynamics of intrinsically disordered polypeptides in solution remains challenging. In this work, we introduce two refined force fields which incorporate either a selective upscaling of protein-water interactions or targeted improvements to backbone torsional sampling: (i) amber ff03w-sc, and (ii) amber ff99SBws-STQ'. Extensive validation against small-angle X-ray scattering (SAXS) and nuclear magnetic reson

SUBMITTER: Phan TM 

PROVIDER: S-EPMC12658220 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature