SCOP database in 2002: refinements accommodate structural genomics

By Loredana Lo Conte, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin. 2002

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Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures (2013, methodology): “The SCOPe website offers a modest redesign of the SCOP website, presenting all SCOPe, SCOP and ASTRAL data through a single, unified web interface.”
The Pfam protein families database (2011, methodology): “Collaborations with the structural protein domain databases SCOP ( 5 ) and CATH (6) have enabled the development of a domain comparison tool to aid this process (see Fig. 1). This tool allows the relationship of the structural domain architecture defined by CATH and SCOP to be compared with each oth”
Data growth and its impact on the SCOP database: new developments (2007, neutral): “uk/ scop/) together with parseable files encoding all SCOP data (3).”
SCOP database in 2004: refinements integrate structure and sequence family data (2004, methodology): “uk/scop/) together with parsable ®les encoding all SCOP data (5).”
Replacement (1980, methodology): “The SCOP database (Murzin et al. , 1995; Lo Conte et al. , 2002) is checked to see whether any of the templates under consideration includes domains; if so, a new template is constructed for those domains.”
Exploiting sequence and structure homologs to identify protein–protein binding sites (2005, unknown): “The pairs containing chains belonging to SCOP class (cid:1) 8 38,39 or less than 80 amino acids long were discarded to ﬁlter out small fragments and focus our attention on relatively large protein– protein interfaces.”
The structure of the protein universe and genome evolution (2002, background): “Nevertheless, there is a wide agreement both on the general principles of classification and on the taxonomic assignments of most protein”
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003 (2003, background): “The membrane protein chain, including a domain deﬁned by the SCOP (4,5), is eliminated by this factor.”
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models (2004, methodology): “For each model, the Repository provides links to the target sequence entry in Swiss-Prot (2), the template structure entries in PDB (1), SCOP (35) and CATH (36), and domain organization in InterPro (37).”
HPID: The Human Protein Interaction Database (2004, background): “29.1 (http://www.ensembl.org/), 3877 yeast proteins, SCOP proteins (Lo Conte et al., 2002) and a non-redundant protein sequence database, NRDB90 (Holm and Sander, 1998).”
The InterPro Database, 2003 brings increased coverage and new features (2003, methodology): “A project has been initiated to rationalise the data of SCOP (Structural Classification of Proteins) (19), CATH (Class, Architecture, Topology, Homology) (20), and SWISS-MODEL 3D structure homology models (21) with that of InterPro.”