Prediction of side-chain conformations on protein surfaces.

ABSTRACT: An approach is described that improves the prediction of the conformations of surface side chains in crystal structures, given the main-chain conformation of a protein. A key element of the methodology involves the use of the colony energy. This phenomenological term favors conformations found in frequently sampled regions, thereby approximating entropic effects and serving to smooth the potential energy surface. Use of the colony energy significantly improves prediction accuracy for surface side chains with little additional computational cost. Prediction accuracy was quantified as the percentage of side-chain dihedral angles predicted to be within 40 degrees of the angles measured by X-ray diffraction. Use of the colony energy in predictions for single side chains improved the prediction

SUBMITTER: Xiang Z 

PROVIDER: S-EPMC2743384 | biostudies-literature | 2007 Mar

REPOSITORIES: biostudies-literature