Using CATH-Gene3D to analyze the UNIT 1.28 sequence, structure, and function of proteins

Current Protocols in Bioinformatics

Volumn 2015, Issue , 2015, Pages 1.28.1-1.28.21

  Sillitoe, Ian ^a   Lewis, Tony ^a   Orengo, Christine ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

Functional family; Protein classification; Protein domain; Protein structure; Superfamily

Indexed keywords

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; ARTICLE; CATH GENE3D DATABASE; ENZYME ACTIVE SITE; EVOLUTION; FACTUAL DATABASE; GENE MUTATION; INTERNET; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATA BANK; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; CHEMISTRY; MOLECULAR GENETICS; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; SEARCH ENGINE;

PROTEIN;

AMINO ACID SEQUENCE; DATABASES, PROTEIN; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEARCH ENGINE;

EID: 84949224197     PISSN: 19343396     EISSN: 1934340X     Source Type: Journal    
DOI: 10.1002/0471250953.bi0128s50     Document Type: Article

References (10)

1. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.E. Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., and Tasumi, M. The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542.
2. Furnham, N., Sillitoe, I., Holliday, G.L., Cuff, A.L., Rahman, S.A., Laskowski, R.A., Orengo, C.A., and Thornton, J.M. 2012. FunTree: A resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucl. Acids Res. 40:D776-D782.
3. Lees, J., Yeats, C., Perkins, J., Sillitoe, I., Rentzsch, R., Dessailly, B.H., and Orengo C. 2012. Gene3D: A domain-based resource for comparative genomics, functional annotation and protein network analysis. Nucl. Acids Res. 40:D465-D471.
4. Redfern, O.C., Harrison, A., Dallman, T., Pearl, F.M., and Orengo, C.A. 2007. CATHEDRAL: A fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. PLoS Comput. Biol. 3(11):e232.
5. Sillitoe, I., Cuff, A.L., Dessailly, B.H., Dawson, N.L., Furnham, N., Lee, D., Lees, J.G., Lewis, T.E., Studer, R.A., Rentzsch, R., Yeats, C., Thornton, J.M., and Orengo, C.A. 2013. New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D Structures. Nucl. Acids Res.:D490-D498.
6. Sillitoe, I., Lewis, T.E., Cuff, A., Das, S., Ashford, P., Dawson, N.L., Furnham, N., Laskowski, R.A., Lee, D., Lees, J.G., Lehtinen, S., Studer, R.A., Thornton, J., and Orengo, C.A. 2015. CATH: Comprehensive structural and functional annotations for genome sequences. Nucl. Acids Res. 43:D376-D381.
7. Supek, F., Bošnjak, M., Škunca, N., and Šmuc T. 2011. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One. 6(7):e21800.
8. Tamuri, A.U. and Laskowski, R.A. 2010. Arch- Schema: A tool for interactive graphing of related Pfamdomain architectures. Bioinformatics 26:1260-1261.
9. Valdar, W.S. 2002. Scoring residue conservation. Proteins 48:227-241.
10. Yeats, C., Redfern, O.C., and Orengo C. 2010. A fast and automated solution for accurately resolving protein domain architectures. Bioinformatics 26:745-751.