Comparison of Protein Active Site Structures for Functional Annotation of Proteins and Drug Design

Authors

Robert Powers, University of Nebraska - LincolnFollow
Jennifer C. Copeland, University of Nebraska - Lincoln
Katherine Germer, University of Nebraska - Lincoln
Kelly A. Mercier, University of Nebraska - Lincoln
Viswanathan Ramanathan, University of Nebraska - Lincoln
Peter Revesz, University of Nebraska - LincolnFollow

Document Type

Article

Date of this Version

July 2006

Comments

Published in PROTEINS: Structure, Function and Bioinformatics 65:1 (2006), pp. 124–135. Published online in Wiley InterScience (www. interscience.wiley.com). DOI: 10.1002/prot.21092 Copyright © 2006 WILEY-LISS Inc. Used by permission.

Abstract

Rapid and accurate functional assignment of novel proteins is increasing in importance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally, global primary-sequence and structure comparisons have been used to determine putative function. These approaches, however, do not emphasize similarities in active site configurations that are fundamental to a protein’s activity and highly conserved relative to the global and more variable structural features. The Comparison of Protein Active Site Structures (CPASS) database and software enable the comparison of experimentally identified ligand-binding sites to infer biological function and aid in drug discovery. The CPASS database comprises the ligand-defined active sites identified in the protein data bank, where the CPASS program compares these ligand-defined active sites to determine sequence and structural similarity without maintaining sequence connectivity. CPASS will compare any set of ligand-defined protein active sites, irrespective of the identity of the bound ligand.