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PIRSF: family classification system at the Protein Information Resource

C. H. Wu
2004 Nucleic Acids Research  
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

Anastasia N. Nikolskaya, Cecilia N. Arighi, Hongzhan Huang, Winona C. Barker, Cathy H. Wu
2006 Evolutionary Bioinformatics  
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

Anastasia N Nikolskaya, Cecilia N Arighi, Hongzhan Huang, Winona C Barker, Cathy H Wu
2007 Evolutionary Bioinformatics  
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

H Huang, ZZ Hu, BE Suzek, CH Wu
2004 Data Science Journal  
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]

Darren A. Natale, C. R. Vinayaka, Cathy H. Wu
2005 Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics  
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

Zhang-Zhi Hu, Inderjeet Mani, Vincent Hermoso, Hongfang Liu, Cathy H. Wu
2004 Computational biology and chemistry  
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

Cathy Wu, Daniel W Nebert
2004 Human Genomics  
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

N. J. Mulder
2004 Nucleic Acids Research  
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

Rajaram Gana, Shruti Rao, Hongzhan Huang, Cathy Wu, Sona Vasudevan
2013 BMC Structural Biology  
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  
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

Chuming Chen, Peter B. McGarvey, Hongzhan Huang, Cathy H. Wu
2010 Advances in Bioinformatics  
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

A. Kuzniar, K. Lin, Y. He, H. Nijveen, S. Pongor, J. A. M. Leunissen
2009 Nucleic Acids Research  
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

Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, Cathy H. Wu
2006 Proceedings of the 1st international workshop on Text mining in bioinformatics - TMBIO '06  
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  
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

Darren A Natale, Cecilia N Arighi, Winona C Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, Cathy H Wu
2007 BMC Bioinformatics  
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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