Docking-based long timescale simulation of cell-size protein systems at atomic resolution.

ABSTRACT: Computational methodologies are increasingly addressing modeling of the whole cell at the molecular level. Proteins and their interactions are the key component of cellular processes. Techniques for modeling protein interactions, thus far, have included protein docking and molecular simulation. The latter approaches account for the dynamics of the interactions but are relatively slow, if carried out at all-atom resolution, or are significantly coarse grained. Protein docking algorithms are far more efficient in sampling spatial coordinates. However, they do not account for the kinetics of the association (i.e., they do not involve the time coordinate). Our proof-of-concept study bridges the two modeling approaches, developing an approach that can reach unprecedented simulation timescales a

SUBMITTER: Vakser IA 

PROVIDER: S-EPMC9565162 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature