Comparison of protein active site structures for functional annotation of proteins and drug design

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. Proteins 2006. © 2006 Wiley‐Liss, Inc.