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PIR-ALN: a database of protein sequence alignments
1999
Bioinformatics
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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
1999
Nucleic Acids Research
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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
1992
Nucleic Acids Research
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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
2001
Nucleic Acids Research
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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
1999
Nucleic Acids Research
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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
2001
Genome Biology
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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
1998
Nucleic Acids Research
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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
1996
Nucleic Acids Research
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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)
2000
Nucleic Acids Research
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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
2000
Nucleic Acids Research
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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
2003
Nucleic Acids Research
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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
1999
Nucleic Acids Research
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.
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
1997
Protein Engineering Design & Selection
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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
2001
Bioinformatics
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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
2001
Bioinformatics
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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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