Designing coarse grained-and atom based-potentials for protein-protein docking.

ABSTRACT:

Background

Protein-protein docking is a challenging computational problem in functional genomics, particularly when one or both proteins undergo conformational change(s) upon binding. The major challenge is to define a scoring function soft enough to tolerate these changes and specific enough to distinguish between near-native and "misdocked" conformations.

Results

Using a linear programming (LP) technique, we developed two types of potentials: (i) Side chain-based and (ii) Heavy atom-based. To achieve this we considered a set of 161 transient complexes and generated a large set of putative docked structures (decoys), based on a shape complementarity criterion, for each complex. The demand on the potentials was to yield, for the native (correctly docked) structure, a potenti

SUBMITTER: Tobi D 

PROVIDER: S-EPMC2996388 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature