Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.

By Julian Gough, Kevin J. Karplus, Richard Hughey, Cyrus Chothia. 2001

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In Molecular Biology

Citations in the corpus

SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures (2013, methodology): “Other methods such as SUPERFAMILY (9,10) and SCOPmap (11) have been developed to automatically classify new PDB structures in the context of SCOP and have the advantage of operating on proteins somewhat dissimilar from those already classified.”
The Universal Protein Resource (UniProt) (2004, background): “InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (14), PROSITE (15), PRINTS (16), ProDom (17), SMART (18), PIRSF (19), Superfamily (20) and TIGRFAMs (21).”
Ranking non-synonymous single nucleotide polymorphisms based on disease concepts (2014, methodology): “In conjunction, protein domains from the SUPERFAMILY [18] and Pfam (Pfam-A and Pfam-B) [19] databases are annotated onto the full-length protein sequence.”
SCOPmap: Automated assignment of protein structures to evolutionary superfamilies (2004, methodology): “Comparison of SCOPmap results and SUPERFAMILY [11] results for the same test set indicates that SCOPmap performs better than SUPERFAMILY both in terms of overall correct assignments and in accurate definition of the domain boundaries of those assignments.”
Fold recognition by combining sequence profiles derived from evolution and from depth‐dependent structural alignment of fragments (2004, background): “For example, Gough et al.(48) found that hidden Markov models (HMM) generated”
InterProScan: protein domains identifier (2005, neutral): “Database members and their applications Database Application ProDom (6) BlastProDom (Blastall) (4) PRINTS (7) FingerPrintScan (8) SMART (9) Hmmpfam (http://hmmer.wustl.edu/) TIGRFAMs (10) Hmmpfam (http://hmmer.wustl.edu/) Pfam (11) Hmmpfam (http://hmmer.wustl.edu/) PROSITE (12) ScanRegExp + ProfileS”
Prediction of protein function from protein sequence and structure (2003, background): “Murzin (1998) and Grishin (2001) have discussed how far divergence can push the relationships between homology, structure and sequence divergence, and functional change.”
SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments (2002, methodology): “The SAM software was used to build a library of models (3) representing all proteins of known structure, which forms the core of the SUPERFAMILY database.”
The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity (2015, background): “…Akeyelementofthisweightingschemeistheuseofthe twoparameters Wn and Wd , which represent the relative frequency of neutral variants ( Wn ) and pathogenic variants ( Wd ) in the relevant protein family, deﬁned through SUPERFAMILY [Gough et al., 2001] or Pfam [Sonnhammer et al., 1997].”
The Ensembl gene annotation system (2016, methodology): “We identify these signatures by both ab initio sequence search [SEG (95), SignalP (96), ncoils (97), TMHMM (98)] and searching protein domain databases for sequence matches [PRINTS (99), Pfscan (100), Pfam (101), TIGRFAM, SUPERFAMILY (102), SMART (103) and PIRSF (104)].”
Benchmarking of Methods for Genomic Taxonomy (2014, methodology): “Brieﬂy, for each genome, functional proﬁles were assigned based on three collections of hidden Markov model (HMM) databases: PfamA (30), TIGRFAM (31), and Su-perfamily(32).”
Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities (2008, methodology): “Several tools and resources are available for such analysis, including BLASTX [26], rsCDS [27], Pfam [28], and SUPERFAMILY [29].”
D2P2: database of disordered protein predictions (2012, neutral): “SUPERFAMILY is a library of hidden Markov models (HMMs) for SCOP structural domain classifications at the superfamily and family level (33).”
SCOP database in 2002: refinements accommodate structural genomics (2002, methodology): “For each domain in the first seven classes, there are links to supplementary information related to that domain in Pfam (9), SUPERFAMILY (6), PartsList (10) and, in case there is one or more sequences predicted to have that fold, to PRESAGE (11).”