SCOP database in 2004: refinements integrate structure and sequence family data

By Antonina Andreeva, Dave Howorth, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia, Alexey G. Murzin. 2004

976 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Computational Biology & Bioinformatics

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

In Molecular Biology

In Computational Biology & Bioinformatics

Citations in the corpus

Discriminative Embeddings of Latent Variable Models for Structured Data (2016, positive): “The first one (denoted as SCOP) contains 7329 sequences obtained from SCOP (Structural Classification of Proteins) 1.59 database (Andreeva et al., 2004).”
The Pfam protein families database (2007, methodology): “In order to improve this situation, we built over 500 new Pfam-A families for PDB sequences and SCOP (Structural Classification of Proteins) database entries (6), which were not previously covered.”
Data growth and its impact on the SCOP database: new developments (2007, neutral): “We have introduced significant changes to the SCOP update protocol since our previous report (10).”
Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners (2007, methodology): “Most methods begin by annotating protein sequences with domains that can be defined by Pfam, SCOP, CDD, or other domain databases [63–65].”
Comparative Protein Structure Modeling Using Modeller (2006, methodology): “The identification of suitable templates is achieved by scanning structure databases, such as PDB (Berman et al., 2000), SCOP (Andreeva et al., 2004), DALI, UNIT 5.5 (Dietmann et al., 2001), and CATH (Pearl et al., 2005), with the target sequence as the query.”
Natively Unstructured Loops Differ from Other Loops (2007, methodology): “Due to the fact that NORSnet is optimized to identify unstructured stretches that are longer than 30 (and SCOP domain boundaries are often shorter), we used the raw score by NORSnet rather than the filtered output.”
InterPro, progress and status in 2005 (2004, background): “Structural domains from SCOP (11) and CATH (12) are made up of one or more protein chains in a PDB entry.”
The SWISS-MODEL Repository: new features and functionalities (2005, methodology): “For each putative template, information about experimental details, likely quaternary structure (24), bound ligands, and links to external structure databases, such as SCOP (25), CATH (26) and MSD (27), are provided accompanied by a small ribbon representation.”
D2P2: database of disordered protein predictions (2012, methodology): “75 version of the HMM library (34) were used to provide predictions of SCOP structural domains (35,36).”
Probabilistic multi-class multi-kernel learning: on protein fold recognition and remote homology detection (2008, methodology): “In Ding and Dubchak (2001) an extensive study on a publicly available data-set, consisting of 27 SCOP folds (Andreeva et al., 2004; Lo Conte et al., 2000), was conducted exploring the use of various multi-class adaptations of the wellknown binary SVM classifier methodology. In that work, the best me”
Understanding eukaryotic linear motifs and their role in cell signaling and regulation. (2008, neutral): “Many bioinformatics tools are also available for studies of globular domains, including SMART, Pfam, CDD, SCOP and CATH (6-10).”
MaGe: a microbial genome annotation system supported by synteny results (2006, background): “Highly sensitive comparison of each predicted protein with the SCOP database of known structural domains (34,35) is also carried out.”