Protein docking along smooth association pathways.

ABSTRACT: We propose a docking method that mimics the way proteins bind. The method accounts for the dominant driving forces at the different length scales of the protein binding process, allowing for an efficient selection of a downhill path on the evolving receptor-ligand-free energy landscape. Starting from encounter complexes with as much as 10 A rms deviation from the native conformation, the method locally samples the six dimensional space of rigid-body receptor-ligand structures subject to a van der Waals constraint. The sampling is initially biased only by the desolvation and electrostatic components of the free energy, which capture the partial affinity of unbound structures that are more than 4 A away from the native state. Below this threshold, improved discrimination is attained by addin

SUBMITTER: Camacho CJ 

PROVIDER: S-EPMC58518 | biostudies-literature | 2001 Sep

REPOSITORIES: biostudies-literature