SCOP: a structural classification of proteins database
By Tim J. P. Hubbard, Alexey G. Murzin, Steven E. Brenner, Cyrus Chothia. 1998
Subfields: Computational Biology & Bioinformatics
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In Computational Biology & Bioinformatics
- Yang Zhang
- Johannes Söding
- Burkhard Rost
- David T. Jones
- Martin Steinegger
- Sean R. Eddy
- Jinbo Xu
- Andrej Sali
Citations in the corpus
- Uniclust databases of clustered and deeply annotated protein sequences and alignments (2016, methodology): “Third, we provide deep annotation of Uniclust sequences with Pfam (11) and SCOP (12) domains, and matches to PDB sequences (13)”
- Hidden Markov model speed heuristic and iterative HMM search procedure (2010, background): “Current datasets of homologous proteins primarily utilize either protein structure or sequence conservation to infer homology [8-10].”
- Rapid 3D protein structure database searching using information retrieval techniques (2004, unknown): “Strictly speaking, the 3D structures stored in ASTRAL are not the whole proteins, but the domains within the proteins according to SCOP (Hubbard et al., 1997) domain definitions.”
- Multi-class protein fold recognition using support vector machines and neural networks (2001, methodology): “As an independent dataset for testing we used the PDB- 40D set developed by the authors of the SCOP database (Lo Conte et al., 2000).”
- Recognition of Structure Classification of Protein Folding by NN and SVM Hierarchical Learning Architecture (2003, methodology): “The test dataset was based on PDB-40D set developed by the authors of the SCOP database [11].”
- Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone (2011, methodology): “Structure-derived sequences are grouped into families using information from the SCOP database [17] by pooling sequences sharing the same SCOP superfamily.”
- An efficient algorithm for large-scale detection of protein families. (2002, methodology): “The SCOP database is a collection of well characterised proteins for which three-dimensional structures are available (47).”