Recapturing Cooperativity of α-Helix Formation and Packing in Coarse-Grained Protein Structure Modeling with Multitorsional Potentials.

ABSTRACT: The multitorsional potential accounting for cooperativity of local interactions proposed in our previous work (Sikorska & Liwo, J. Phys. Chem. B, 2022, 126, 9493-9505; 2023, 127, 425-426) has been introduced into the UNRES coarse-grained force field. The parameters of the potential have been found by means of maximum-likelihood principle using the data of 1,092,517 helical segments of protein structures of the Protein Data Bank. The modified UNRES has been tested with a set of 28 α-helical proteins with size from 20 to 126 amino acid residues and various topologies. With the best parametrization, the first-choice models were significantly improved for 10 proteins (ΔGDT_TS > 5) and deteriorated for 3 proteins (ΔGDT_TS < -5). The improvement resulted from strengthening o

SUBMITTER: Petrusevich EF 

PROVIDER: S-EPMC12278218 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature