Ligand-binding site prediction of proteins based on known fragment-fragment interactions.

ABSTRACT:

Motivation

The identification of putative ligand-binding sites on proteins is important for the prediction of protein function. Knowledge-based approaches using structure databases have become interesting, because of the recent increase in structural information. Approaches using binding motif information are particularly effective. However, they can only be applied to well-known ligands that frequently appear in the structure databases.

Results

We have developed a new method for predicting the binding sites of chemically diverse ligands, by using information about the interactions between fragments. The selection of the fragment size is important. If the fragments are too small, then the patterns derived from the binding motifs cannot be used, since they are many-body inter

SUBMITTER: Kasahara K 

PROVIDER: S-EPMC2881410 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature