Pre- and post-docking sampling of conformational changes using ClustENM and HADDOCK for protein-protein and protein-DNA systems.

ABSTRACT: Incorporating the dynamic nature of biomolecules in the modeling of their complexes is a challenge, especially when the extent and direction of the conformational changes taking place upon binding is unknown. Estimating whether the binding of a biomolecule to its partner(s) occurs in a conformational state accessible to its unbound form ("conformational selection") and/or the binding process induces conformational changes ("induced-fit") is another challenge. We propose here a method combining conformational sampling using ClustENM-an elastic network-based modeling procedure-with docking using HADDOCK, in a framework that incorporates conformational selection and induced-fit effects upon binding. The extent of the applied deformation is estimated from its energetical costs, inspired from m

SUBMITTER: Kurkcuoglu Z 

PROVIDER: S-EPMC6973081 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature