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The Protein Information Resource

C. H. Wu
2003 Nucleic Acids Research  
The Protein Information Resource (PIR) is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery.  ...  PIR maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283 000 sequences covering the entire taxonomic range.  ...  ACKNOWLEDGEMENT The PIR is supported by grant P41 LM05978 from the National Library of Medicine, National Institutes of Health.  ... 
doi:10.1093/nar/gkg040 pmid:12520019 pmcid:PMC165487 fatcat:tkixiygtdvg7vjpo6xsbz34qte

The Protein Information Resource (PIR)

W. C. Barker
2000 Nucleic Acids Research  
The Protein Information Resource (PIR) produces the largest, most comprehensive, annotated protein sequence database in the public domain, the PIR-International Protein Sequence Database, in collaboration  ...  with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Sequence Database (JIPID).  ...  The work at MIPS is supported by the Federal Ministry of Education, Science, Research and Technology (BMBF, FKZ 03311670, 01KW9703/7), the Max-Planck-Society and the European Commission (BIO4-CT96-0110  ... 
doi:10.1093/nar/28.1.41 pmid:10592177 pmcid:PMC102418 fatcat:jmqdvezniratdgfskh5llytmua

The Protein Information Resource: an integrated public resource of functional annotation of proteins

C. H. Wu
2002 Nucleic Acids Research  
The Protein Information Resource (PIR) serves as an integrated public resource of functional annotation of protein data to support genomic/proteomic research and scientific discovery.  ...  The PIR, in collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japan International Protein Information Database (JIPID), produces the PIR-International Protein Sequence  ...  The PIR is supported by grant P41 LM05978 from the National Library of Medicine, National Institutes of Health.  ... 
doi:10.1093/nar/30.1.35 pmid:11752247 pmcid:PMC99125 fatcat:prcjea53zrcj3bhdd2yvoydagi

The Universal Protein Resource (UniProt): an expanding universe of protein information

C. H. Wu
2006 Nucleic Acids Research  
The Universal Protein Resource (UniProt) provides a central resource on protein sequences and functional annotation with three database components, each addressing a key need in protein bioinformatics.  ...  The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/ TrEMBL section, is the preeminent storehouse of protein  ...  PIR activities are also supported by the NIH grants for NIAID proteomic resource (HHSN266200400061C) and grid enablement (NCI-caBIG-ICR-10-10-01) and National Science Foundation grants for iProClass (DBI  ... 
doi:10.1093/nar/gkj161 pmid:16381842 pmcid:PMC1347523 fatcat:6xrpacost5entptndstyr7gnry

The Protein Information Resource (PIR) and the PIR-International Protein Sequence Database

D. G. George, R. J. Dodson, J. S. Garavelli, D. H. Haft, L. T. Hunt, C. R. Marzec, B. C. Orcutt, K. E. Sidman, G. Y. Srinivasarao, L.-S. L. Yeh, L. M. Arminski, R. S. Ledley (+2 others)
1997 Nucleic Acids Research  
From its origin, the PIR has aspired to support research in computational biology and genomics through the compilation of a comprehensive, quality controlled and well-organized protein sequence information  ...  The resource originated with the pioneering work of the late Margaret O. Dayhoff in the early 1960s.  ...  Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the National Library of Medicine.  ... 
doi:10.1093/nar/25.1.24 pmid:9016497 pmcid:PMC146415 fatcat:3dgqdeps6vglrlamwglkltwdvq

PIRSF: family classification system at the Protein Information Resource

C. H. Wu
2004 Nucleic Acids Research  
The PIRSF system provides a comprehensive resource for bioinformatics analysis and comparative studies of protein function and evolution.  ...  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:10.1093/nar/gkh097 pmid:14681371 pmcid:PMC308831 fatcat:tr72ubcszncfdmbv4sc7lwpsym

The Protein Model Portal—a comprehensive resource for protein structure and model information

Juergen Haas, Steven Roth, Konstantin Arnold, Florian Kiefer, Tobias Schmidt, Lorenza Bordoli, Torsten Schwede
2013 Database: The Journal of Biological Databases and Curation  
The Protein Model Portal-a comprehensive resource for protein structure and model information.  ...  The Protein Model Portal (PMP) has been developed to foster effective use of 3D molecular models in biomedical research by providing convenient and comprehensive access to structural information for proteins  ...  Acknowledgements We would like to thank Helen Berman, John Westbrook and the SBKB team for stimulating discussions and inspiration.  ... 
doi:10.1093/database/bat031 pmid:23624946 pmcid:PMC3889916 fatcat:acu4ceij6raabopjz4l2pxnkvi

The PRINTS Database of Protein Fingerprints: A Novel Information Resource for Computational Molecular Biology

T. K. Attwood, H. Avison, M. E. Beck, M. Bewley, A. J. Bleasby, F. Brewster, P. Cooper, K. Degtyarenko, A. J. Geddes, D. R. Flower, M. P. Kelly, S. Lott (+6 others)
1997 Journal of chemical information and computer sciences  
PRINTS is a compendium of protein motif fingerprints derived from the OWL composite sequence database.  ...  The current version, 14.0, encodes 3500 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on.  ...  The project benefits from use of the BBSRC SEQNET facility.  ... 
doi:10.1021/ci960468e pmid:9177000 fatcat:grmdrgamczc5dhj3yekolsfieu

The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information

M. B. Arnaud
2004 Nucleic Acids Research  
CGD is a public resource for the research community that is interested in the molecular biology of this fungus.  ...  The Candida Genome Database (CGD) is a new database that contains genomic information about the opportunistic fungal pathogen Candida albicans.  ...  ACKNOWLEDGEMENTS CGD thanks the Candida Annotation Working Group, especially Andre Nantel, for their generosity in sharing their entire data set and their enthusiasm for letting CGD house this resource  ... 
doi:10.1093/nar/gki003 pmid:15608216 pmcid:PMC539957 fatcat:uyutdlkpene2tjbz53prj5qcwe

YPDTM, PombePDTM and WormPDTM: model organism volumes of the BioKnowledgeTM Library, an integrated resource for protein information

M. C. Costanzo
2001 Nucleic Acids Research  
Each Protein Report on the web site summarizes and displays published information about a single protein, including its biochemical function, role in the cell and in the whole organism, localization, mutant  ...  The relevance of these comprehensively curated resources to analysis of proteins in other species is discussed, and is illustrated by a survey of model organism proteins that have similarity to human proteins  ...  We also thank the staffs of the Saccharomyces Genome Database (http://genome-www.stanford.edu/ Saccharomyces), the Munich Information Centre for Protein Sequences (http://www.mips.biochem.mpg.de), the  ... 
doi:10.1093/nar/29.1.75 pmid:11125054 pmcid:PMC29810 fatcat:64s4nxfgifhnrdkcwk7u2uambi

HSPIR: a manually annotated heat shock protein information resource

Ratheesh Kumar R., Nagarajan N. S., Arunraj S. P., Devanjan Sinha, Vinoth Babu Veedin Rajan, Vinoth Kumar Esthaki, Patrick D'Silva
2012 Computer applications in the biosciences : CABIOS  
Heat shock protein information resource (HSPIR) is a concerted database of six major heat shock proteins (HSPs), namely, Hsp70, Hsp40, Hsp60, Hsp90, Hsp100 and small HSP.  ...  GenBank, Protein Data Bank and the literature.  ...  Funding: This work was supported by the Wellcome Trust International Senior Research Fellowship in Biomedical Science (WT081643MA to P.D.S.) and support from Indian Institute of Science, Bangalore.  ... 
doi:10.1093/bioinformatics/bts520 pmid:22923302 pmcid:PMC3476333 fatcat:cxu2eye77ze4bhj4mizlt6qz4e

The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information

M. C. Costanzo
2000 Nucleic Acids Research  
The Yeast Proteome Database (YPD™) has been for several years a resource for organized and accessible information about the proteins of Saccharomyces cerevisiae.  ...  In both databases, information gleaned from the literature is presented in a consistent, user-friendly Protein Report format: a single Web page presenting all available knowledge about a particular protein  ...  ACKNOWLEDGEMENTS We thank the staff of the Saccharomyces Genome Database (http://genome-www.stanford.edu/Saccharomyces ), the Munich Information Centre for Protein Sequences (http://www. mips. biochem.mpg.de  ... 
doi:10.1093/nar/28.1.73 pmid:10592185 pmcid:PMC102421 fatcat:peejgnzoezfkzmlwrw7zdkjgmm

The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family

R. T. Moreland, J. F. Ryan, C. Pan, A. D. Baxevanis
2009 Database: The Journal of Biological Databases and Curation  
The Homeodomain Resource is a curated collection of sequence, structure, interaction, genomic and functional information on the homeodomain family.  ...  The current version builds upon previous versions by the addition of new, complete sets of homeodomain sequences from fully sequenced genomes, the expansion of existing curated homeodomain information  ...  This research was supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health. Conflict of interest. None declared.  ... 
doi:10.1093/database/bap004 pmid:20157477 pmcid:PMC2790301 fatcat:bw6tfpww2nftlnhxaagpu54qgm

PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families

O. Krishnadev, N. Rekha, S. B. Pandit, S. Abhiman, S. Mohanty, L. S. Swapna, S. Gore, N. Srinivasan
2005 Nucleic Acids Research  
Unique features of PRODOC include the generation of alignments between multi-domain proteins on the basis of the sequence of domains and in-built information on distantly related domain families forming  ...  The in-built dataset currently consists of $698 000 proteins from 192 organisms with complete genomic data, and all the SWISSPROT proteins obtained from the Pfam database.  ...  This information is used in the domain architecture search tool to result in the identification of distantly related multidomain proteins with one or more domains related by a superfamily connection (  ... 
doi:10.1093/nar/gki474 pmid:15980440 pmcid:PMC1160235 fatcat:wwyginneorahxjghg7abl5eira

The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community

Martha B. Arnaud, Marcus C. Chibucos, Maria C. Costanzo, Jonathan Crabtree, Diane O. Inglis, Adil Lotia, Joshua Orvis, Prachi Shah, Marek S. Skrzypek, Gail Binkley, Stuart R. Miyasato, Jennifer R. Wortman (+1 others)
2009 Nucleic Acids Research  
The Aspergillus Genome Database (AspGD) is an online genomics resource for researchers studying the genetics and molecular biology of the Aspergilli.  ...  AspGD combines high-quality manual curation of the experimental scientific literature examining the genetics and molecular biology of Aspergilli, cutting-edge comparative genomics approaches to iteratively  ...  ACKNOWLEDGEMENTS We would like to thank CADRE for data exchange and support, SGD for providing their code base and the Aspergillus research community for giving us their support and the opportunity to  ... 
doi:10.1093/nar/gkp751 pmid:19773420 pmcid:PMC2808984 fatcat:nfra65frajdqnmywomhkshr7kq
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