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An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database
- 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
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Cited by 944 (19 self)
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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
Pfam protein families database
- 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
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Cited by 771 (13 self)
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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 GenPept
BioSCAN: A Network Sharable Computational Resource for Searching Biosequence Databases
, 1996
"... We describe a network sharable, interactive computational tool for rapid and sensitive search and analysis of biomolecular sequence databases such as GenBank, GenPept, Protein Identification Resource, and SWISS-PROT. The resource is accessible via the World Wide Web using popular client software suc ..."
Abstract
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Cited by 7 (1 self)
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We describe a network sharable, interactive computational tool for rapid and sensitive search and analysis of biomolecular sequence databases such as GenBank, GenPept, Protein Identification Resource, and SWISS-PROT. The resource is accessible via the World Wide Web using popular client software
doi:10.1093/nar/gkr922 MimoDB 2.0: a mimotope database and beyond
, 2011
"... Mimotopes are peptides with affinities to given targets. They are readily obtained through biopanning against combinatorial peptide libraries constructed by phage display and other display technologies such as mRNA display, ribosome display, bacterial display and yeast display. Mimotopes have been u ..."
Abstract
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Cited by 2 (1 self)
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used to infer the protein interaction sites and networks; they are also ideal candidates for developing new diagnostics, therapeutics and vaccines. However, such valuable peptides are not collected in the central data resources such as UniProt and NCBI GenPept due to their ‘unnatural ’ short sequences
DOI: 10.1093/nar/gkg040 The Protein Information Resource
, 2002
"... The Protein Information Resource (PIR) is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery. PIR maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283 000 sequences covering the entire ..."
Abstract
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The Protein Information Resource (PIR) is an integrated public resource of protein informatics that supports genomic and proteomic research and scientific discovery. PIR maintains the Protein Sequence Database (PSD), an annotated protein database containing over 283 000 sequences covering
¡ Corresponding author.
, 1997
"... 1 The increasing size of protein sequence databases is straining methods of sequence analysis, even as the increased information offers opportunities for sophisticated analyses of protein structure, function and evolution. Here we describe a method called Meta-MEME that uses artificial intelligence- ..."
Abstract
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1 The increasing size of protein sequence databases is straining methods of sequence analysis, even as the increased information offers opportunities for sophisticated analyses of protein structure, function and evolution. Here we describe a method called Meta-MEME that uses artificial intelligence
Identification of a Novel Cysteine-stack Arrangement in Parallel β-helix Proteins using Computational and Knowledge-based Approach
, 2007
"... Abstract Parallel β-helices, a subclass of β-sheet proteins, represent the folding of a polypeptide chain into an elongated topologically simpler fold than globular β-sheets. However, the amino acid sequence rules that specify β-sheet structure in protein remain unelucidated. In this study, a combi ..."
Abstract
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-like protein families displaying this pattern, and to produce high confidence 3D models for all detectable members of this superfamily. To achieve these goals, candidate sequences were retrieved from GenPept and SUPERFAMILY databases. Possible pectin lyase-like proteins were detected with two different fold
Conservation and Variability of West Nile Virus Proteins
"... West Nile virus (WNV) has emerged globally as an increasingly important pathogen for humans and domestic animals. Studies of the evolutionary diversity of the virus over its known history will help to elucidate conserved sites, and characterize their correspondence to other pathogens and their relev ..."
Abstract
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and their relevance to the immune system. We describe a large-scale analysis of the entire WNV proteome, aimed at identifying and characterizing evolutionarily conserved amino acid sequences. This study, which used 2,746 WNV protein sequences collected from the NCBI GenPept database, focused on analysis of peptides
