Structural modeling of protein interactions by analogy: application to PSD-95.

ABSTRACT: We describe comparative patch analysis for modeling the structures of multidomain proteins and protein complexes, and apply it to the PSD-95 protein. Comparative patch analysis is a hybrid of comparative modeling based on a template complex and protein docking, with a greater applicability than comparative modeling and a higher accuracy than docking. It relies on structurally defined interactions of each of the complex components, or their homologs, with any other protein, irrespective of its fold. For each component, its known binding modes with other proteins of any fold are collected and expanded by the known binding modes of its homologs. These modes are then used to restrain conventional molecular docking, resulting in a set of binary domain complexes that are subsequently ranked by g

SUBMITTER: Korkin D 

PROVIDER: S-EPMC1635541 | biostudies-literature | 2006 Nov

REPOSITORIES: biostudies-literature