SCOP: a structural classification of proteins database for the investigation of sequences and structures.

By Alexey G. Murzin, Steven E. Brenner, Tim J. P. Hubbard, Cyrus Chothia. 1995

Subfields: Evaluation & Benchmarks, Computational Biology & Bioinformatics

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Citations in the corpus

ECOD: An Evolutionary Classification of Protein Domains (2014, background): “Currently, the two leading structure classifications are SCOP (Structural Classification of Proteins) [4] and CATH (Class, Architecture, Topology, Homology) [5], both of which are widely used in analyzing protein sequence, structure, function, and evolution and in developing various bioinformatics t”
Improvement of molecular-replacement models with Sculptor (2011, methodology): “A preliminary study suite containing four target structures was selected from the benchmark suite (one from each SCOP class) and used to explore the effect of algorithm parameters Acta Cryst.”
Learning protein sequence embeddings using information from structure (2019, background): “Methods for finding proteins with related structure directly from sequence are of considerable interest, but the problem is challenging, because sequence similarity and structural similarity are only loosely related [1, 2, 3, 4], e.”
DeepSF: deep convolutional neural network for mapping protein sequences to folds (2017, methodology): “The protein sequences for each SCOP domain were cleaned according to the observed residues in the atomic structures [2].”
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields (2014, methodology): “In total we use a set of 1400 protein pairs as the training and validation data, which covers 458 SCOP folds [30].”
SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures (2013, methodology): “The SCOP database was first released in December 1994 and contained all 3091 entries in the PDB at that time (1).”
TM-align: a protein structure alignment algorithm based on the TM-score (2005, positive): “For example, many authors use SCOP (1) or CATH (2) as the gold standard and assess the structural alignments based on the fold classi-ﬁcations in these databases (23–25).”
The Pfam protein families database (2007, methodology): “The domain boundaries used are currently those defined by the SCOP database (6) and a new web-based tool allows direct cross-linking from domains on the SCOP web site to the corresponding Pfam families.”
The Pfam protein families database (2011, methodology): “The domain boundaries used are currently those defined by the SCOP database ( 6 ) and a new web-based tool allows direct cross-linking from domains on the SCOP web site to the corresponding Pfam families.”
MMseqs2: sensitive protein sequence searching for the analysis of massive data sets (2017, background): “tural domains [19] with 25% maximal pairwise sequence identity.”
The HHpred interactive server for protein homology detection and structure prediction (2005, background): “The N-terminal domain has two signiﬁcant hits in SCOP at rank 1 and 3.”
Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics (2015, neutral): “In another study, researchers used motifs from protein interactions for detecting Structural Classification of Proteins (SCOP) [19] families for 368 proteins, and obtained a classification accuracy of 75% at sensitivity of 10% [20].”
Data growth and its impact on the SCOP database: new developments (2007, neutral): “The Structural Classification of Proteins (SCOP) is a database of known structural and evolutionary relationships amongst proteins of known structure (1).”
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure (2018, background): “A non-redundant dataset designed in a way so that every SCOP family [77] has at most one typical representative and to minimize the number of unannotated binding sites (by superimposing ligands from very close homologs).”
Template-based protein structure modeling using the RaptorX web server (2012, background): “Current methods do, however, become unreliable when there are no homologs with solved structures in PDB or when templates under consideration are distant homologs 16 .”