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PIR-ALN: a database of protein sequence alignments

G. Y. Srinivasarao, L. S. Yeh, C. R. Marzec, B. C. Orcutt, W. C. Barker
1999 Bioinformatics  
Results: Release 22.0, (December 1998), of the PIR-ALN database contains a total of 3806 alignments, including 1303 superfamily, 2131 family and 372 homology domain alignments.  ...  Motivation: The Protein Information Resource (PIR) maintains a database of annotated and curated alignments in order to visually represent interrelationships among sequences in the PIR-International Protein  ...  The authors thank PIR staff for their contributions of alignments to the database and Kathryn Sidman for administrative support.  ... 
doi:10.1093/bioinformatics/15.5.382 pmid:10366659 fatcat:jv5js5zwfbgxbfqd6kd3szcx5i

Database of protein sequence alignments: PIR-ALN

G. Y. Srinivasarao, L.-S. L. Yeh, C. R. Marzec, B. C. Orcutt, W. C. Barker, F. Pfeiffer
1999 Nucleic Acids Research  
The Protein Information Resource (PIR) has been maintaining a database of curated protein sequence alignments since 1991. The collection includes superfamily, family and homology domain alignments.  ...  The database has helped in classifying sequences, in defining new homology domains, and in spreading and standardizing protein names, features and keywords among members of a family or superfamily.  ...  The authors thank PIR staff for their contributions of alignments to the database and Katie Sidman and Desiree Goins for administrative support and help with Web page design.  ... 
doi:10.1093/nar/27.1.284 pmid:9847202 pmcid:PMC148157 fatcat:7zjhne6z6zewdldkcuu63lqynm

The PIR-International Protein Sequence Database

W. C. Barker, D. G. George, H.-W. Mewes, A. Tsugita
1992 Nucleic Acids Research  
The weekly release of the Protein Sequence Database can be accessed through the PIR Web site.  ...  The PIR Protein Sequence Database entries are classified into superfamilies, families and homology domains, for which sequence alignments are available.  ...  PIR is a registered mark of the NBRF.  ... 
doi:10.1093/nar/20.suppl.2023 pmid:1375994 pmcid:PMC333980 fatcat:pk66vyryyfb5vaugsej5ij3bna

iProClass: an integrated, comprehensive and annotated protein classification database

C. H. Wu
2001 Nucleic Acids Research  
It is extended from ProClass, a protein family database that integrates PIR superfamilies and PROSITE motifs.  ...  The database facilitates classification-driven annotation for protein sequence databases and complete genomes, and supports structural and functional genomic research.  ...  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

The PIR-International Protein Sequence Database

W. C. Barker, J. S. Garavelli, P. B. McGarvey, C. R. Marzec, B. C. Orcutt, G. Y. Srinivasarao, L.-S. L. Yeh, R. S. Ledley, H.-W. Mewes, F. Pfeiffer, A. Tsugita, C. Wu
1999 Nucleic Acids Research  
The weekly release of the Protein Sequence Database can be accessed through the PIR Web site.  ...  The PIR Protein Sequence Database entries are classified into superfamilies, families and homology domains, for which sequence alignments are available.  ...  PIR is a registered mark of the NBRF.  ... 
doi:10.1093/nar/27.1.39 pmid:9847137 pmcid:PMC148092 fatcat:uq7zz564e5f6vkhnb76u5t4wcy

Tools and resources for identifying protein families, domains and motifs

Nicola J Mulder, Rolf Apweiler
2001 Genome Biology  
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.  ...  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.  ...  Other major alignment databases are: PIR-ALN [26, 27] , which is a database of annotated protein sequence alignments derived automatically from the PIR sequence database and has alignments at the superfamily  ... 
pmid:11806833 pmcid:PMC150457 fatcat:jqx7k7zk5jbe7pp3nrg22lo32e

The PIR-International Protein Sequence Database

W. Barker
1998 Nucleic Acids Research  
controlled, and well-organized protein sequence database.  ...  during a period of explosive acquisition of new data.  ...  Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the National Library of Medicine. PIR is a registered mark of the NBRF.  ... 
doi:10.1093/nar/26.1.27 pmid:9399794 pmcid:PMC147240 fatcat:mpbgtbyxa5bvvobxtyg2euuk6y

The PIR-International Protein Sequence Database

D. George
1996 Nucleic Acids Research  
controlled, and well-organized protein sequence database.  ...  during a period of explosive acquisition of new data.  ...  Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the National Library of Medicine. PIR is a registered mark of the NBRF.  ... 
doi:10.1093/nar/24.1.17 pmid:8594572 pmcid:PMC145575 fatcat:x24ghg3fnzd55cluciiwo33hbm

The Protein Information Resource (PIR)

W. C. Barker
2000 Nucleic Acids Research  
The expanded PIR WWW site allows sequence similarity and text searching of the Protein Sequence Database and auxiliary databases.  ...  Several new web-based search engines combine searches of sequence similarity and database annotation to facilitate the analysis and functional identification of proteins.  ...  ACKNOWLEDGEMENTS PIR is a registered mark of NBRF. The work at NBRF is supported by grant number P41 LM05978 from the National Library of Medicine and by gifts from COMPAQ, Pfizer and Dupont.  ... 
doi:10.1093/nar/28.1.41 pmid:10592177 pmcid:PMC102418 fatcat:jmqdvezniratdgfskh5llytmua

ProClass protein family database

H. Huang
2000 Nucleic Acids Research  
ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PIR superfamilies and PROSITE patterns.  ...  To maximize family information retrieval, the database provides links to various protein family, domain, alignment and structural class databases.  ...  To maximize family information retrieval, ProClass provides hypertext links to major family databases, including family and superfamily alignments [PIR-ALN (7) and ProtFam (8)], motif and domain databases  ... 
doi:10.1093/nar/28.1.273 pmid:10592245 pmcid:PMC102450 fatcat:jip4gszgpbdn3eir46o5folofe

SDAP: database and computational tools for allergenic proteins

O. Ivanciuc
2003 Nucleic Acids Research  
SDAP (Structural Database of Allergenic Proteins) is a web server that provides rapid, cross-referenced access to the sequences, structures and IgE epitopes of allergenic proteins.  ...  , PIR-ALN, NCBI Taxonomy Browser) and literature (PubMed, MEDLINE) on-line servers.  ...  The current lists of allergens were assembled from literature and from major sequence [SWISS-PROT/TrEMBL (18), PIR-ALN (19) and NCBI Taxonomy Browser (20) ] and structure [PDB (21) ] databases, guided  ... 
doi:10.1093/nar/gkg010 pmid:12520022 pmcid:PMC165457 fatcat:mavfzylbh5godjeibbkzqaf6w4

ProClass Protein Family Database

C. H. Wu, S. Shivakumar, H. Huang
1999 Nucleic Acids Research  
ProClass is a protein family database that organizes non-redundant sequence entries into families defined collectively by PIR superfamilies and PROSITE patterns.  ...  To maximize family information retrieval, the database provides links to various protein family, domain, alignment and structural class databases.  ...  To maximize family information retrieval, ProClass provides hypertext links to major family databases, including family and superfamily alignments [PIR-ALN (7) and ProtFam (8)], motif and domain databases  ... 
doi:10.1093/nar/27.1.272 pmid:9847199 pmcid:PMC148154 fatcat:447qhu5nbbf3nkozvg2rsdj6ry

Amino acid substitutions preserve protein folding by conserving steric and hydrophobicity properties

I. Ladunga, R. F. Smith
1997 Protein Engineering Design & Selection  
across widely different databases and alignment methods reflect  ...  The PIR-ALN database (George et al., 1996) globally Still, the most frequent SPs follow very similar distributions aligns selected superfamilies of the Protein Identification in most databases irrespective  ...  PIMA and PIR-ALN databases and by fewer than 400 SPs in the sequences (as measured by the proportion of fully conserved positions, Figure 1 and Table I) .  ... 
doi:10.1093/protein/10.3.187 pmid:9153083 fatcat:yksxxojl25ejjah6qwsizacr5a

MetaFam: a unified classification of protein families. I. Overview and statistics

K. A. T. Silverstein, E. Shoop, J. E. Johnson, E. F. Retzel
2001 Bioinformatics  
MetaFam is a protein family classification built upon 10 publicly-accessible protein family databases (Blocks+, DOMO, Pfam, PIR-ALN, PRINTS, PROSITE, ProDom, PROTOMAP, SBASE, and SYSTERS).  ...  Motivation: Protein sequence classification is becoming an increasingly important means of organizing the voluminous data produced by large-scale genome sequencing projects.  ...  the Department of Energy (DOE) Pine Gene Discovery Project, #DE-FC07 97ID13550; the United Soybean Board and the United States Department of Agriculture (USDA) Public EST Project for Soybean, #58-3625-  ... 
doi:10.1093/bioinformatics/17.3.249 pmid:11294790 fatcat:2k6kvfjewbhzfber2fsaav5624

MetaFam: a unified classification of protein families. II. Schema and query capabilities

E. Shoop, K. A. T. Silverstein, J. E. Johnson, E. F. Retzel
2001 Bioinformatics  
MetaFam is a protein family classification built upon 10 publicly-accessible protein family databases (Blocks+, DOMO, Pfam, PIR-ALN, PRINTS, PROSITE, ProDom, PROTOMAP, SBASE, and SYSTERS).  ...  Motivation: Protein sequence classification is becoming an increasingly important means of organizing the voluminous data produced by large-scale genome sequencing projects.  ...  the Department of Energy (DOE) Pine Gene Discovery Project, #DE-FC07 97ID13550; the United Soybean Board and the United States Department of Agriculture (USDA) Public EST Project for Soybean, #58-3625-  ... 
doi:10.1093/bioinformatics/17.3.262 pmid:11294791 fatcat:zkjrvhdswna6jgn2eramanvo24
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