Molecular Dynamics Scoring of Protein-Peptide Models Derived from Coarse-Grained Docking.

ABSTRACT: One of the major challenges in the computational prediction of protein-peptide complexes is the scoring of predicted models. Usually, it is very difficult to find the most accurate solutions out of the vast number of sometimes very different and potentially plausible predictions. In this work, we tested the protocol for Molecular Dynamics (MD)-based scoring of protein-peptide complex models obtained from coarse-grained (CG) docking simulations. In the first step of the scoring procedure, all models generated by CABS-dock were reconstructed starting from their original C-alpha trace representations to all-atom (AA) structures. The second step included geometry optimization of the reconstructed complexes followed by model scoring based on receptor-ligand interaction energy estimated from sho

SUBMITTER: Zalewski M 

PROVIDER: S-EPMC8197827 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature