Native or Non-Native Protein-Protein Docking Models? Molecular Dynamics to the Rescue.

ABSTRACT: Molecular docking excels at creating a plethora of potential models of protein-protein complexes. To correctly distinguish the favorable, native-like models from the remaining ones remains, however, a challenge. We assessed here if a protocol based on molecular dynamics (MD) simulations would allow distinguishing native from non-native models to complement scoring functions used in docking. To this end, the first models for 25 protein-protein complexes were generated using HADDOCK. Next, MD simulations complemented with machine learning were used to discriminate between native and non-native complexes based on a combination of metrics reporting on the stability of the initial models. Native models showed higher stability in almost all measured properties, including the key ones used for sc

SUBMITTER: Jandova Z 

PROVIDER: S-EPMC8444332 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature