title: Comparison of protein active site structures for functional annotation of proteins and drug design.
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.
authors.affiliation: Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA. rpowers3@unl.edu
authors.forename: Robert
authors.initials: R
authors.lastname: Powers
authors.forename: Jennifer C
authors.initials: JC
authors.lastname: Copeland
authors.forename: Katherine
authors.initials: K
authors.lastname: Germer
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Mercier
authors.forename: Viswanathan
authors.initials: V
authors.lastname: Ramanathan
authors.forename: Peter
authors.initials: P
authors.lastname: Revesz
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D001665:Binding Sites; D030562:Databases, Protein; D015195:Drug Design; D008024:Ligands; D011506:Proteins / Q000737:chemistry* / Q000502:physiology; D011732:Pyridoxal Phosphate / Q000378:metabolism; D012985:Software Design
chemical_list: D008024:Ligands; D011506:Proteins; D011732:Pyridoxal Phosphate; D000255:Adenosine Triphosphate