CASP5 target classification
- PMID: 14579323
- PMCID: PMC2656935
- DOI: 10.1002/prot.10555
CASP5 target classification
Abstract
This report summarizes the Critical Assessment of Protein Structure Prediction (CASP5) target proteins, which included 67 experimental models submitted from various structural genomics efforts and independent research groups. Throughout this special issue, CASP5 targets are referred to with the identification numbers T0129-T0195. Several of these targets were excluded from the assessment for various reasons: T0164 and T0166 were cancelled by the organizers; T0131, T0144, T0158, T0163, T0171, T0175, and T0180 were not available in time; T0145 was "natively unfolded"; the T0139 structure became available before the target expired; and T0194 was solved for a different sequence than the one submitted. Table I outlines the sequence and structural information available for CASP5 proteins in the context of existing folds and evolutionary relationships. This information provided the basis for a domain-based classification of the target structures into three assessment categories: comparative modeling (CM), fold recognition (FR), and new fold (NF). The FR category was further subdivided into homologues [FR(H)] and analogs [FR(A)] based on evolutionary considerations, and the overlap between assessment categories was classified as CM/FR(H) and FR(A)/NF. CASP5 domains are illustrated in Figure 1. Examples of nontrivial links between CASP5 target domains and existing structures that support our classifications are provided.
Copyright 2003 Wiley-Liss, Inc.
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References
-
- Schlessman JL, Woo D, Joshua-Tor L, Howard JB, Rees DC. Conformational variability in structures of the nitrogenase iron proteins from Azotobacter vinelandii and Clostridium pasteurianum. J Mol Biol. 1998;280:669–685. - PubMed
-
- van den Akker F. Structural insights into the ligand binding domains of membrane bound guanylyl cyclases and natriuretic peptide receptors. J Mol Biol. 2001;311:923–937. - PubMed
-
- Hickman AB, Namboodiri MA, Klein DC, Dyda F. The structural basis of ordered substrate binding by serotonin N-acetyltransferase: enzyme complex at 1.8 A resolution with a bisubstrate analog. Cell. 1999;97:361–369. - PubMed
-
- Angus-Hill ML, Dutnall RN, Tafrov ST, Sternglanz R, Ramakrishnan V. Crystal structure of the histone acetyltransferase Hpa2: a tetrameric member of the Gcn5-related N-acetyltransferase superfamily. J Mol Biol. 1999;294:1311–1325. - PubMed
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