PIRSF: family classification system at the Protein Information Resource

By Cathy H. Wu, Anastasia N. Nikolskaya, Hongzhan Huang, L. Yeh, D. Natale, C. R. Vinayaka, Zhang-Zhi Hu, R. Mazumder, Sandeep Kumar, P. Kourtesis and 10 more. 2004

234 citations recorded by the source corpus.

Subfields: Molecular Biology

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Citations in the corpus

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches (2014, neutral): “UniRef entries contain”
The Universal Protein Resource (UniProt) (2004, background): “To exploit known structure information, site rules are deﬁned starting with PIRSF families that contain at least one known three-dimensional (3D) structure with experimentally veri-ﬁed site information.”
InterPro in 2017—beyond protein family and domain annotations (2016, background): “The integration of similar residue-level annotations from databases like Pfam and PIRSF, coupled with highly specific subfamily-level annotations from resources like PANTHER and PRINTS, extends this functionality even further.”
HMMER web server: 2018 update (2018, methodology): “The existing profile HMM libraries (Pfam (2), CATH-Gene3D (16), TIGRFAMs (17), Superfamily (18) and PIRSF (19)) have been supplemented by those of the TreeFam (20) database of phylogenetic trees.”
clusterMaker: a multi-algorithm clustering plugin for Cytoscape (2011, background): “A third use of clustering is the identification of similar groups of proteins for the purpose of classification [10], that is, inferring properties of proteins of unknown function based on their similarity to proteins of known function.”
HMMER web server: 2015 update (2015, methodology): “Furthermore, the HMMER3 based protein family databases CATH-Gene3D (20), PIRSF (21), Superfamily (22) and TIGRFAMs (23) have been incorporated into the hmmscan search as alternative target HMM databases.”
UniProt: the Universal Protein knowledgebase (2004, background): “InterPro is an integrated resource of protein families, domains and sites that amalgamates the efforts of the member databases: Pfam (11), PROSITE (12), PRINTS (13), ProDom (14), SMART (15), PIRSF ( 16 ), Superfamily (17) and TIGRFAMs (18).”
New developments in the InterPro database (2007, methodology): “Reference InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER.”
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)].”
PIRSF Family Classification System for Protein Functional and Evolutionary Analysis (2006, background): “With experimentally verifi ed information on protein function lagging far behind, computational methods are needed for reliable and large-scale functional annotation of proteins.”
The PANTHER database of protein families, subfamilies, functions and pathways (2004, methodology): “PANTHER HMMs have also been mapped to existing PIRSF (15) entries, and a collaboration is currently underway to make PANTHER and PIRSF consistent and crossreferenced.”
InterProScan 5: genome-scale protein function classification (2014, methodology): “As InterProScan 5 makes use of the Hibernate object-relational mapping tool (http://www.hibernate.org/), it should be possible to port the back-end to run on most relational database management systems.”
The Universal Protein Resource (UniProt) 2009 (2008, methodology): “The computer-assisted annotation is created using automatically generated rules as in Spearmint (2), or manually curated rules based on protein families, including HAMAP family rules (3), RuleBase rules (4) and PIRSF classification-based name rules and site rules ( 5 ,6).”
The RAST Server: Rapid Annotations using Subsystems Technology (2008, background): “A number of groups have spent substantial effort building protein families that now represent resources that are widely used and valued by the community [11-15]; see [16] for a more extended discussion.”
The HMMER Web Server for Protein Sequence Similarity Search (2017, methodology): “…Lewis, & Orengo, 2015); Superfamily comprises domain annotations of protein sequences predicted using the HMM libraries based on SCOP superfamilies (Wilson et al., 2009); and the PIRSF database comprises HMMs for comprehensive non-overlapping clustering of protein sequences (Wu et al., 2004).”
InterProScan: protein domains identifier (2005, background): “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 + ProfileScan (13) PIRSF ( 14 ) Hmmpfam (http://hmmer.wustl.edu/) SUPER”
SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny (2008, unknown): “The InterPro consortium integrates databases of protein families, domains and functional sites, including: Gene3D (30), PANTHER (31), Pfam (32), PIRSF ( 33 ), PRINTS (34), ProDom (35), PROSITE (36), SMART (37), SUPERFAMILY and TIGRFAMs (38).”