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iProClass: an integrated database of protein family, function and structure information

H. Huang
2003 Nucleic Acids Research  
The protein information in iProClass includes family relationships as well as structural and functional classifications and features.  ...  It provides rich links to over 50 database of protein sequences, families, functions and pathways, proteinprotein interactions, post-translational modifications, protein expressions, structures and structural  ...  ACKNOWLEDGEMENTS This study is supported by grant DBI-9974855 and DBI-0138188 from National Science Foundation, and grant P41 LM05798 from National Library of Medicine.  ... 
doi:10.1093/nar/gkg044 pmid:12520030 pmcid:PMC165491 fatcat:7yw5d3gsczelhlqyx7hbofpwau

The iProClass integrated database for protein functional analysis

Cathy H Wu, Hongzhan Huang, Anastasia Nikolskaya, Zhangzhi Hu, Winona C Barker
2004 Computational biology and chemistry  
Coupled with the underlying taxonomic information for complete genomes, the iProClass system ( supports associative studies of protein family, domain, function, and  ...  of protein family, function, pathway, interaction, modification, structure, genome, ontology, literature, and taxonomy.  ...  Acknowledgements The project is supported by grant DBI-0138188 from National Science Foundation and grant U01-HG02712 from National Institutes of Health.  ... 
doi:10.1016/j.compbiolchem.2003.10.003 pmid:15022647 fatcat:kkzflwqewfablaw4y2vkmxvzzm

iProClass: an integrated, comprehensive and annotated protein classification database

C. H. Wu
2001 Nucleic Acids Research  
The iProClass database is an integrated resource that provides comprehensive family relationships and structural and functional features of proteins, with rich links to various databases.  ...  sites and links to more than 30 databases of protein families, structures, functions, genes, genomes, literature and taxonomy.  ...  ACKNOWLEDGEMENTS This study is supported in part by grant DBI-9974855 from National Science Foundation, and grant P41 LM05798 from National Library of Medicine, NIH.  ... 
doi:10.1093/nar/29.1.52 pmid:11125047 pmcid:PMC29833 fatcat:bzntvv4tqzgafb52jdyvbp6ev4


Cathy H. Wu, Winona C. Barker
2004 The Practical Bioinformatician  
The Protein Information Resource (PIR) ¼¿ provides an integrated public resource of protein informatics to support genomic and proteomic research and scientific discovery.  ...  PIR produces the Protein Sequence Database (PSD) of functionally annotated protein sequences, which grew out of the Atlas of Protein Sequence and Structure edited by Margaret Dayhoff. ½ ½ The annotation  ...  The iProClass database is supported by DBI-9974855 from the National Science Foundation.  ... 
doi:10.1142/9789812562340_0019 fatcat:l7agtzoktbailpq6y3z7oqckma

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.  ...  as structural and functional classifications and features of proteins.  ... 
doi:10.2481/dsj.3.163 fatcat:dzvrwfkazfbzddrch6vcfkcwiy

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.  ...  Comprehensive protein information is available from i ProClass, which includes family classification at the superfamily, domain and motif levels, structural and functional features of proteins, as well  ...  The iProClass and RESID databases are supported by DBI-9974855 and DBI-9808414 from the National Science Foundation.  ... 
doi:10.1093/nar/30.1.35 pmid:11752247 pmcid:PMC99125 fatcat:prcjea53zrcj3bhdd2yvoydagi

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  ...  Acknowledgments This study is supported in part by Grants U01HG02712 and HHSN266200400061C. 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

Protein family classification and functional annotation

Cathy H Wu, Hongzhan Huang, Lai-Su L Yeh, Winona C Barker
2003 Computational biology and chemistry  
family, function, and structure information, provides extensive value-added features for about 830,000 proteins with rich links to over 50 molecular databases.  ...  PIR-NREF, a non-redundant reference database, provides a timely and comprehensive collection of all protein sequences, totaling more than 1,000,000 entries. iProClass, an integrated database of protein  ...  The iProClass database is supported by DBI-9974855 and DBI-0138188 from National Science Foundation.  ... 
doi:10.1016/s1476-9271(02)00098-1 pmid:12798038 fatcat:krl4xfssurbwzeajazhe47frfu

Update on genome completion and annotations: Protein Information Resource

Cathy Wu, Daniel W Nebert
2004 Human Genomics  
Data integration and associative studies of protein family, function and structure are supported by the iProClass database, which offers value-added descriptions of all UniProt proteins with highly informative  ...  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  ...  Acknowledgments The PIR is supported by grant U01 HG02712 from the National Institutes of Health and grants DBI-0138188 and ITR-0205470 from the National Science Foundation (C.W.).  ... 
doi:10.1186/1479-7364-1-3-229 pmid:15588483 pmcid:PMC3525084 fatcat:w6btvshqf5g3zakh53dzjoryku

The Protein Information Resource

C. H. Wu
2003 Nucleic Acids Research  
PIR also maintains NREF, a non-redundant reference database, and iProClass, an integrated database of protein family, function, and structure information.  ...  The Protein Information Resource (PIR) is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery.  ...  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

Systems Integration of Biodefense Omics Data for Analysis of Pathogen-Host Interactions and Identification of Potential Targets

Peter B. McGarvey, Hongzhan Huang, Raja Mazumder, Jian Zhang, Yongxing Chen, Chengdong Zhang, Stephen Cammer, Rebecca Will, Margie Odle, Bruno Sobral, Margaret Moore, Cathy H. Wu (+1 others)
2009 PLoS ONE  
The availability of pathogen and host omics data in an integrated framework allows global analysis of the data and comparisons across different experiments and organisms, as illustrated in several case  ...  The integrative analysis across data sets from multiple centers can reveal potential functional significance and hidden relationships between pathogen and host proteins, thereby providing a systems approach  ...  of protein attributes, including information on the encoding genes, protein families, pathways, functions and more.  ... 
doi:10.1371/journal.pone.0007162 pmid:19779614 pmcid:PMC2745575 fatcat:y4asrpywyfhy5ppbrknppx34nu

An emerging cyberinfrastructure for biodefense pathogen and pathogen host data

C. Zhang, O. Crasta, S. Cammer, R. Will, R. Kenyon, D. Sullivan, Q. Yu, W. Sun, R. Jha, D. Liu, T. Xue, Y. Zhang (+8 others)
2007 Nucleic Acids Research  
The web-interface for the database enables searching, querying and downloading at the level of experiment, group and individual gene(s)/ protein(s) via UniProtKB accession numbers or protein function keywords  ...  All of the genes/proteins are annotated and integrated across experiments using UniProt Knowledgebase (UniProtKB) accession numbers.  ...  ACKNOWLEDGEMENTS The authors appreciate comments and suggestions from Terry Brennan, Shamira Shallom, Joe Breen, Malu Polanski and JoJo Stemple. This work is funded through  ... 
doi:10.1093/nar/gkm903 pmid:17984082 pmcid:PMC2239001 fatcat:fglzouvstjhgpaii2rqb67bspu

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

C. H. Wu
2006 Nucleic Acids Research  
UniProt databases continue to grow in size and in availability of information. Recent and upcoming changes to database contents, formats, controlled vocabularies and services are described.  ...  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.  ...  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

Tools and resources for identifying protein families, domains and motifs

Nicola J Mulder, Rolf Apweiler
2001 Genome Biology  
This article reviews the tools and resources available on the web for identifying signatures within proteins and discusses how they may be used in the analysis of new or unknown protein sequences.  ...  With the large influx of raw sequence data from genome sequencing projects, there is a need for reliable automatic methods for protein sequence analysis and classification.  ...  documentation resource for protein families, domains [49] and functional sites IProClass Integrated protein classification database  ... 
pmid:11806833 pmcid:PMC150457 fatcat:jqx7k7zk5jbe7pp3nrg22lo32e

Using schema transforation pathways for biological data integration

Hao Fan, Fei Wang
2008 Journal of Biomedical Science and Engineering  
databases receive more and more attentions in proteomics research, which strives to provide a high level of annotation, such as the description of the function of a protein, its domains structure, post-translational  ...  modifications variants, etc., a minimal level of redundancy and high level of integration with other databases [2] .  ...  protein domains and classifications: iProClass (see provides an integrated view of protein information and serves as a bioinformatics framework for data integration  ... 
doi:10.4236/jbise.2008.13035 fatcat:bzvbldadwbcofmrka7dxuwtcdi
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