Shape-Restrained Modeling of Protein-Small-Molecule Complexes with High Ambiguity Driven DOCKing.

ABSTRACT: Small-molecule docking remains one of the most valuable computational techniques for the structure prediction of protein-small-molecule complexes. It allows us to study the interactions between compounds and the protein receptors they target at atomic detail in a timely and efficient manner. Here, we present a new protocol in HADDOCK (High Ambiguity Driven DOCKing), our integrative modeling platform, which incorporates homology information for both receptor and compounds. It makes use of HADDOCK's unique ability to integrate information in the simulation to drive it toward conformations, which agree with the provided data. The focal point is the use of shape restraints derived from homologous compounds bound to the target receptors. We have developed two protocols: in the first, the shape

SUBMITTER: Koukos PI 

PROVIDER: S-EPMC8479858 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature