Resolving Molecular Interactions in Protein Folding Trajectories with NCIPLOT.

ABSTRACT: Noncovalent interactions (NCIs) are fundamental to the structure, stability, and function of proteins. These interactions form complex networks that control how different protein regions relate to each other or to external molecules (e.g., solvent, ligands, cofactors, other proteins), shaping the energy landscape of the system. Molecular dynamics (MD) simulations are widely used to study proteins and other biomolecules, helping to explore their structures and transitions between them at atomic resolution. However, the analysis of MD trajectories is often limited to the estimation of geometric features or metrics relating instantaneous configurations to reference structures, which may overlook relevant details of the interactions that drive conformational changes. In this work, we propose a

SUBMITTER: Urriolabeitia A 

PROVIDER: S-EPMC12529773 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature