K-Means Clustering Coarse-Graining (KMC-CG): A Next Generation Methodology for Determining Optimal Coarse-Grained Mappings of Large Biomolecules.

ABSTRACT: Coarse-grained (CG) molecular dynamics (MD) has become a method of choice for simulating various large scale biomolecular processes; therefore, the systematic definition of the CG mappings for biomolecules remains an important topic. Appropriate CG mappings can significantly enhance the representability of a CG model and improve its ability to capture critical features of large biomolecules. In this work, we present a systematic and more generalized method called K-means clustering coarse-graining (KMC-CG), which builds on the earlier approach of essential dynamics coarse-graining (ED-CG). KMC-CG removes the sequence-dependent constraints of ED-CG, allowing it to explore a more extensive space and thus enabling the discovery of more physically optimal CG mappings. Furthermore, the i

SUBMITTER: Wu J 

PROVIDER: S-EPMC10720621 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature