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The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999

by Amos Bairoch, Rolf Apweiler - Nucleic Acids Res , 1999
"... SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other ..."
Abstract - Cited by 619 (5 self) - Add to MetaCart
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000

by Amos Bairoch, Rolf Apweiler - Nucleic Acids Res , 2000
"... SWISS-PROT is a curated protein sequence database 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 othe ..."
Abstract - Cited by 761 (21 self) - Add to MetaCart
SWISS-PROT is a curated protein sequence database 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

The swiss-prot protein knowledgebase and its supplement trembl in 2003

by Brigitte Boeckmann, Amos Bairoch, Rolf Apweiler, Marie-claude Blatter, Anne Estreicher, Elisabeth Gasteiger, Maria J. Martin, Karine Michoud, Isabelle Phan, Rine Pilbout, Michel Schneider - Nucleic Acids Res , 2003
"... The SWISS-PROT protein knowledgebase ..."
Abstract - Cited by 733 (15 self) - Add to MetaCart
The SWISS-PROT protein knowledgebase

amino acid sequence similarities

by Amos Bairocht
"... New families in the classification of glycosyl hydrolases based on amino acid sequence similarities HENRISSAT, Bernard, BAIROCH, Amos Marc 301 glycosyl hydrolases and related enzymes corresponding to 39 EC entries of the I.U.B. classification system have been classified into 35 families on the basis ..."
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of 482 sequences corresponding to 52 EC entries, 45 families, out of which 22 are polyspecific, can now be defined. This classification has been implemented in the SWISS-PROT protein sequence data bank. HENRISSAT, Bernard, BAIROCH, Amos Marc. New families in the classification of glycosyl hydrolases

Database verification studies of SWISS-PROT and

by Peter D. Karp, Suzanne Paley, Jingchun Zhu
"... Problem statement: We have studied the relationships among SWISS-PROT, TrEMBL, and GenBank with two goals. First is to determine whether users can reliably identify those proteins in SWISS-PROT whose functions were determined experimentally, as opposed to proteins whose functions were predicted comp ..."
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Problem statement: We have studied the relationships among SWISS-PROT, TrEMBL, and GenBank with two goals. First is to determine whether users can reliably identify those proteins in SWISS-PROT whose functions were determined experimentally, as opposed to proteins whose functions were predicted

The Protein Data Bank

by Helen M. Berman, John Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne - Nucleic Acids Res , 2000
"... The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the futur ..."
Abstract - Cited by 1339 (23 self) - Add to MetaCart
The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans

NCBI reference sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

by Kim D. Pruitt, Tatiana Tatusova, Donna R. Maglott - Nucleic Acids Res , 2005
"... transcripts and proteins ..."
Abstract - Cited by 586 (6 self) - Add to MetaCart
transcripts and proteins

2005 MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res

by Kazutaka Katoh, Kei-ichi Kuma, Hiroyuki Toh, Takashi Miyata
"... The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement opti-ons, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed hig ..."
Abstract - Cited by 788 (5 self) - Add to MetaCart
database. Such improvement was gen-erally observed for most methods, but remarkably large for the new options of MAFFT proposed here. Thus, we made a Ruby script, mafftE.rb, which aligns the input sequences together with their close homo-logues collected from SwissProt using NCBI-BLAST.

This release of SWISS-PROT has been prepared by:

by Amos Bairoch, Rolf Apweiler, Elisabeth Gasteiger, Alain Gateau, Vivienne Gerritsen, Arnaud Gos, Nadine Gruaz-gumowski, Shyamala Sundaram, Anne-lise Veuthey, Julia Williams-nef, Nadine Zangger, Evguenia Kriventseva, Fiona Lang, Minna Lehvaslaiho, Michele Magrane, Maria Jesus Martin, Virginie Mittard, Steffen Moeller, Nicola Mulder, Tom Oinn, Isabelle Phan, Rine Pilbout, Lucia Rodriguez-monge, Margaret Shore-nye, Eleanor Whitfield , 2000
"... Williams and Evgueni Zdobnov at the European Bioinformatics Institute (EBI). SWISS-PROT contains sequences translated from the EMBL Nucleotide Sequence Database, prepared by the European Bioinformatics Institute. For a recent reference see: Baker W., van den Broek A., Camon E., Hingamp P., Sterk P., ..."
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Williams and Evgueni Zdobnov at the European Bioinformatics Institute (EBI). SWISS-PROT contains sequences translated from the EMBL Nucleotide Sequence Database, prepared by the European Bioinformatics Institute. For a recent reference see: Baker W., van den Broek A., Camon E., Hingamp P., Sterk P

Pfam protein families database

by Robert D. Finn, John Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman - Nucleic Acids Research, 2008, 36(Database issue): D281–D288
"... Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenP ..."
Abstract - Cited by 748 (13 self) - Add to MetaCart
Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI Gen
Results 1 - 10 of 866,247