Chapter 4. Predicting and characterizing protein functions through matching geometric and evolutionary patterns of binding surfaces.

ABSTRACT: Predicting protein functions from structures is an important and challenging task. Although proteins are often thought to be packed as tightly as solids, closer examination based on geometric computation reveals that they contain numerous voids and pockets. Most of them are of random nature, but some are binding sites providing surfaces to interact with other molecules. A promising approach for function prediction is to infer functions through discovery of similarity in local binding pockets, as proteins binding to similar substrates/ligands and carrying out similar functions have similar physical constraints for binding and reactions. In this chapter, we describe computational methods to distinguish those surface pockets that are likely to be involved in important biological functions, an

SUBMITTER: Liang J 

PROVIDER: S-EPMC2882714 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature