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PIRSF: family classification system at the Protein Information Resource
2004
Nucleic Acids Research
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The PIRSF protein classification system (http://pir.georgetown.edu/pirsf/) reflects evolutionary relationships of full-length proteins and domains. ...
The PIRSF system provides a comprehensive resource for bioinformatics analysis and comparative studies of protein function and evolution. ...
Acknowledgements The project is supported by grant U01-HG02712 from the National Institutes of Health and grant DBI-0138188 from the National Science Foundation. ...
doi:10.1093/nar/gkh097
pmid:14681371
pmcid:PMC308831
fatcat:tr72ubcszncfdmbv4sc7lwpsym
PIRSF Family Classification System for Protein Functional and Evolutionary Analysis
2006
Evolutionary Bioinformatics
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studies via the PIRSF web site at ...
The PIRSF protein classification system (http://pir.georgetown.edu/pirsf/) reflects evolutionary relationships of full-length proteins and domains. ...
Acknowledgements The project is supported by grant U01-HG02712 from the National Institutes of Health and grant DBI-0138188 from the National Science Foundation. ...
doi:10.1177/117693430600200033
fatcat:diybosyvjng3phlhk3bsd3oh7m
PIRSF family classification system for protein functional and evolutionary analysis
2007
Evolutionary Bioinformatics
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The PIRSF protein classification system (http://pir.georgetown.edu/pirsf/) reflects evolutionary relationships of full-length proteins and domains. ...
The PIRSF system provides a comprehensive resource for bioinformatics analysis and comparative studies of protein function and evolution. ...
Acknowledgements The project is supported by grant U01-HG02712 from the National Institutes of Health and grant DBI-0138188 from the National Science Foundation. ...
pmid:19455212
pmcid:PMC2674652
fatcat:iw43ynucnbew7p7beebwk2ormq
The PIR integrated protein databases and data retrieval system
2004
Data Science Journal
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PIR also provides PIRSF family classification system based on evolutionary relationships of full-length proteins, and iProClass integrated database of protein family, function, and structure. ...
The Protein Information Resource (PIR) provides many databases and tools to support genomic and proteomic research. ...
PIRSF protein family classification system Protein family classification has been central to the annotation activities PIR since the pioneering work of Margaret Dayhoff. ...
doi:10.2481/dsj.3.163
fatcat:dzvrwfkazfbzddrch6vcfkcwiy
Large-scale, classification-driven, rule-based functional annotation of proteins
[chapter]
2005
Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
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Rule-based annotation will be discussed in the context of the PIRSF protein classification system, PIRNR Name Rule system, and the PIRSR Site Rule system. ...
A more accurate, consistent, and comprehensive approach for largescale automated annotation makes use of protein family classification-driven rules. ...
Acknowledgments The project is supported by grant U01-HG02712 from National Institutes of Health and grant DBI-0138188 from National Science Foundation.
Related articles g306302 ...
doi:10.1002/047001153x.g403314
fatcat:lhwkwad26zcttpgw5be2h5eijq
iProLINK: an integrated protein resource for literature mining
2004
Computational biology and chemistry
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Motivated by the promise of text mining methodologies, but at the same time, the lack of adequate curated data for training and benchmarking, the Protein Information Resource (PIR) has developed a resource ...
as a protein ontology based on PIRSF protein family names. iProLINK is freely accessible at http://pir.georgetown.edu/iprolink, with hypertext links for all downloadable files. ...
Acknowledgements The project is supported by grants ITR-0205470, DBI-0138188, and IIS-0430743 from the National Science Foundation and grant U01-HG02712 from the National Institutes of Health, USA. ...
doi:10.1016/j.compbiolchem.2004.09.010
pmid:15556482
fatcat:nqbne4m6gbdgffgcrm7gf2pfty
Update on genome completion and annotations: Protein Information Resource
2004
Human Genomics
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The PIRSF (SuperFamily) classification system is central to the PIR/UniProt functional annotation of proteins, providing classifications of whole proteins into a network structure to reflect their evolutionary ...
The Protein Information Resource (PIR) recently joined the European Bioinformatics Institute (EBI) and Swiss Institute of Bioinformatics (SIB) to establish UniProt -the Universal Protein Resource -which ...
The writing of this article was funded, in part, by NIH grant P30 ES06096 (D.W.N.). The author very much appreciates the graphics assistance of Dr Marian Miller. ...
doi:10.1186/1479-7364-1-3-229
pmid:15588483
pmcid:PMC3525084
fatcat:w6btvshqf5g3zakh53dzjoryku
InterPro, progress and status in 2005
2004
Nucleic Acids Research
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InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. ...
New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. ...
ACKNOWLEDGEMENTS The InterPro project is supported by the ProFuSe grant (number QLG2-CT-2000-00517) and the Integr8 grant (number QLRI-CT-2001000015) of the European Commission. ...
doi:10.1093/nar/gki106
pmid:15608177
pmcid:PMC540060
fatcat:ykhpocbakfck3elxzhjb7z34rm
Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach
2013
BMC Structural Biology
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Results: Our analysis included 1,224 structures that belong to 172 unique families of the Protein Information Resource Superfamily system. ...
This extends the existing structural classification of SAM binding proteins. ...
Alison Hickman of NIH for critical reading of the manuscript. We thank all members, past and present, of the Protein Information Resource for valuable suggestions and support. ...
doi:10.1186/1472-6807-13-6
pmid:23617634
pmcid:PMC3662625
fatcat:a7j3vo7ha5gjdgx7pcpdlcwf54
The Universal Protein Resource (UniProt)
2007
Nucleic Acids Research
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The UniProt Consortium is a collaboration between the European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB). ...
The Universal Protein Resource (UniProt) provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation. ...
UniProtKB/Swiss-Prot activities at the SIB are supported by the Swiss Federal Government through the Federal Office of Education and Science, by the European Commission contract FELICS (021902RII3) and ...
doi:10.1093/nar/gkl929
pmid:17142230
pmcid:PMC1669721
fatcat:3doko4bysfhmzddimueyp2tj3y
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data
2010
Advances in Bioinformatics
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In this paper, we present the challenges in high-throughput "omics" data integration and analysis, introduce a protein-centric approach for systems integration of large and heterogeneous high-throughput ...
"omics" data including microarray, mass spectrometry, protein sequence, protein structure, and protein interaction data, and use scientific case study to illustrate how one can use varied "omics" data ...
The authors would like to thank the anonymous reviewers for their constructive comments on the manuscript. ...
doi:10.1155/2010/423589
pmid:20369061
pmcid:PMC2847380
fatcat:poilhj6yvvhk7oy45v6ryhroge
ProGMap: an integrated annotation resource for protein orthology
2009
Nucleic Acids Research
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Protein families ...
, TRIBES and PIRSF. ...
ACKNOWLEDGEMENTS The authors thank Hong Luo for expert help in the initial set-up of the Oracle database and Blaise Alako for stimulating discussions. ...
doi:10.1093/nar/gkp462
pmid:19494185
pmcid:PMC2703891
fatcat:gqtya47xbfcmbmg4rcpwo3qa7e
Framework for a protein ontology
2006
Proceedings of the 1st international workshop on Text mining in bioinformatics - TMBIO '06
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The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic ...
Biomedical ontologies are emerging as critical tools in genomic and proteomic research, where complex data in disparate resources need to be integrated. ...
Clusters of homologous proteins: PIRSF The PIRSF family classification system provides protein classification from superfamily to subfamily levels in a network structure to reflect the evolutionary relationship ...
doi:10.1145/1183535.1183544
fatcat:5xofoicamzboxp3cjmnfziwmqa
PIRSitePredict for protein functional site prediction using position-specific rules
2019
Database: The Journal of Biological Databases and Curation
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Methods to provide fine-grained 'local' annotation of functional sites (at the level of individual amino acid) are now coming to the forefront, especially in light of the rapid accumulation of genetic ...
Methods focused on predicting 'global' annotations for proteins (such as molecular function, biological process and presence of domains or membership in a family) have reached a relatively mature stage ...
We also thank our colleagues at the UniProt Consortium for their support. ...
doi:10.1093/database/baz026
pmid:30805646
pmcid:PMC6389862
fatcat:pthry2g4wjbjdlro7kysxmdoxe
Framework for a Protein Ontology
2007
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic ...
Biomedical ontologies are emerging as critical tools in genomic and proteomic research, where complex data in disparate resources need to be integrated. ...
Clusters of homologous proteins: PIRSF The PIRSF family classification system provides protein classification from superfamily to subfamily levels in a network structure to reflect the evolutionary relationship ...
doi:10.1186/1471-2105-8-s9-s1
pmid:18047702
pmcid:PMC2217659
fatcat:z7k56eb7rvcntbqzq2fadogcsq
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