Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles.

ABSTRACT: Accommodating backbone flexibility continues to be the most difficult challenge in computational docking of protein-protein complexes. Towards that end, we simulate four distinct biophysical models of protein binding in RosettaDock, a multiscale Monte-Carlo-based algorithm that uses a quasi-kinetic search process to emulate the diffusional encounter of two proteins and to identify low-energy complexes. The four binding models are as follows: (1) key-lock (KL) model, using rigid-backbone docking; (2) conformer selection (CS) model, using a novel ensemble docking algorithm; (3) induced fit (IF) model, using energy-gradient-based backbone minimization; and (4) combined conformer selection/induced fit (CS/IF) model. Backbone flexibility was limited to the smaller partner of the complex, struct

SUBMITTER: Chaudhury S 

PROVIDER: S-EPMC2573042 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature