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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 624 (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 773 (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

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

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 1387 (24 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

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

Hidden Markov models in computational biology: applications to protein modeling

by Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjölander, David Haussler - JOURNAL OF MOLECULAR BIOLOGY , 1994
"... Hidden.Markov Models (HMMs) are applied t.0 the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated the on globin family, the protein kinase catalytic domain, and the EF-hand calcium binding moti ..."
Abstract - Cited by 655 (39 self) - Add to MetaCart
motif. In each case the parameters of an HMM are estimated from a training set of unaligned sequences. After the HMM is built, it is used to obtain a multiple alignment of all the training sequences. It is also used to search the. SWISS-PROT 22 database for other sequences. that are members of the given

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

by Jimmy K. Eng, Ashley L. Mccormack, John R. Yates - J. Am. Soc. Mass Spectrom , 1994
"... A method to correlate the uninterpreted tandem mass spectra of peptides produced under low energy (lo-50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. In this method the protein database is searched to identify linear amino acid sequences within a mas ..."
Abstract - Cited by 944 (19 self) - Add to MetaCart
A method to correlate the uninterpreted tandem mass spectra of peptides produced under low energy (lo-50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. In this method the protein database is searched to identify linear amino acid sequences within a

Data Security

by Dorothy E. Denning, Peter J. Denning , 1979
"... The rising abuse of computers and increasing threat to personal privacy through data banks have stimulated much interest m the techmcal safeguards for data. There are four kinds of safeguards, each related to but distract from the others. Access controls regulate which users may enter the system and ..."
Abstract - Cited by 615 (3 self) - Add to MetaCart
The rising abuse of computers and increasing threat to personal privacy through data banks have stimulated much interest m the techmcal safeguards for data. There are four kinds of safeguards, each related to but distract from the others. Access controls regulate which users may enter the system

SCOP: a structural classification of proteins database for the investigation of sequences and structures.

by Tim J P Hubbard , Bart Ailey , Steven E Brenner , Alexey G Murzin , Cyrus Chothia - J. Mol. Biol. , 1995
"... ABSTRACT The Structural Classification of Proteins (SCOP) database provides a detailed and comprehensive description of the relationships of all known proteins structures. The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary ..."
Abstract - Cited by 1552 (24 self) - Add to MetaCart
relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. The database can be used as a source of data to calibrate sequence search

Muscle: multiple sequence alignment with high accuracy and high throughput

by Robert C. Edgar - NUCLEIC ACIDS RES , 2004
"... We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using tree-dependent r ..."
Abstract - Cited by 2509 (7 self) - Add to MetaCart
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using tree
Results 1 - 10 of 9,828