Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock.

ABSTRACT: The formation of specific protein-protein interactions is often a key to a protein's function. During complex formation, each protein component will undergo a change in the conformational state, for some these changes are relatively small and reside primarily at the sidechain level; however, others may display notable backbone adjustments. One of the classic problems in the protein-docking field is to be able to a priori predict the extent of such conformational changes. In this work, we investigated three protocols to find the most suitable input structure conformations for cross-docking, including a robust sampling approach in normal mode space. Counterintuitively, knowledge of the theoretically best combination of normal modes for unbound-bound transitions does not always lead to the be

SUBMITTER: Torchala M 

PROVIDER: S-EPMC7496321 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature