Literature DB >> 15215409

CysView: protein classification based on cysteine pairing patterns.

Johann Lenffer1, Paulo Lai, Wafaa El Mejaber, Asif M Khan, Judice L Y Koh, Paul T J Tan, Seng H Seah, Vladimir Brusic.   

Abstract

CysView is a web-based application tool that identifies and classifies proteins according to their disulfide connectivity patterns. It accepts a dataset of annotated protein sequences in various formats and returns a graphical representation of cysteine pairing patterns. CysView displays cysteine patterns for those records in the data with disulfide annotations. It allows the viewing of records grouped by connectivity patterns. CysView's utility as an analysis tool was demonstrated by the rapid and correct classification of scorpion toxin entries from GenPept on the basis of their disulfide pairing patterns. It has proved useful for rapid detection of irrelevant and partial records, or those with incomplete annotations. CysView can be used to support distant homology between proteins. CysView is publicly available at http://research.i2r.a-star.edu.sg/CysView/.

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Year:  2004        PMID： 15215409      PMCID： PMC441613          DOI： 10.1093/nar/gkh475

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  37 in total

Review 1.  Scorpion toxins specific for Na+-channels.

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Journal:  Eur J Biochem       Date:  1999-09

2.  DNA data bank of Japan (DDBJ) in collaboration with mass sequencing teams.

Authors:  Y Tateno; S Miyazaki; M Ota; H Sugawara; T Gojobori
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

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Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

Review 4.  The cystine knot motif in toxins and implications for drug design.

Authors:  D J Craik; N L Daly; C Waine
Journal:  Toxicon       Date:  2001-01       Impact factor: 3.033

5.  Classification of protein disulphide-bridge topologies.

Authors:  J M Mas; P Aloy; M A Martí-Renom; B Oliva; R de Llorens; F X Avilés; E Querol
Journal:  J Comput Aided Mol Des       Date:  2001-05       Impact factor: 3.686

6.  13C NMR chemical shifts can predict disulfide bond formation.

Authors:  D Sharma; K Rajarathnam
Journal:  J Biomol NMR       Date:  2000-10       Impact factor: 2.835

7.  Oxidative folding of proteins.

Authors:  M Narayan; E Welker; W J Wedemeyer; H A Scheraga
Journal:  Acc Chem Res       Date:  2000-11       Impact factor: 22.384

Review 8.  What can venom phospholipases A(2) tell us about the functional diversity of mammalian secreted phospholipases A(2)?

Authors:  E Valentin; G Lambeau
Journal:  Biochimie       Date:  2000 Sep-Oct       Impact factor: 4.079

Review 9.  Disulfide bonds and protein folding.

Authors:  W J Wedemeyer; E Welker; M Narayan; H A Scheraga
Journal:  Biochemistry       Date:  2000-04-18       Impact factor: 3.162

10.  Respiratory chain strongly oxidizes the CXXC motif of DsbB in the Escherichia coli disulfide bond formation pathway.

Authors:  T Kobayashi; K Ito
Journal:  EMBO J       Date:  1999-03-01       Impact factor: 11.598
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  13 in total

1.  HCA and HML isolated from the red marine algae Hypnea cervicornis and Hypnea musciformis define a novel lectin family.

Authors:  Celso S Nagano; Henri Debray; Kyria S Nascimento; Vicente P T Pinto; Benildo S Cavada; Silvana Saker-Sampaio; Wladimir R L Farias; Alexandre H Sampaio; Juan J Calvete
Journal:  Protein Sci       Date:  2005-08       Impact factor: 6.725

2.  Solution structure of the phytotoxic protein PcF: the first characterized member of the Phytophthora PcF toxin family.

Authors:  Giuseppe Nicastro; Giuseppe Orsomando; Elena Ferrari; Lucia Manconi; Filomena Desario; Adolfo Amici; Alessia Naso; Armando Carpaneto; Thelma A Pertinhez; Silverio Ruggieri; Alberto Spisni
Journal:  Protein Sci       Date:  2009-08       Impact factor: 6.725

3.  Amino acid patterns around disulfide bonds.

Authors:  José R F Marques; Rute R da Fonseca; Brett Drury; André Melo
Journal:  Int J Mol Sci       Date:  2010-11-18       Impact factor: 5.923

4.  Hyperdimensional analysis of amino acid pair distributions in proteins.

Authors:  Svend B Henriksen; Rasmus J Mortensen; Henrik M Geertz-Hansen; Maria Teresa Neves-Petersen; Omar Arnason; Jón Söring; Steffen B Petersen
Journal:  PLoS One       Date:  2011-12-09       Impact factor: 3.240

5.  DISULFIND: a disulfide bonding state and cysteine connectivity prediction server.

Authors:  Alessio Ceroni; Andrea Passerini; Alessandro Vullo; Paolo Frasconi
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

6.  ClanTox: a classifier of short animal toxins.

Authors:  Guy Naamati; Manor Askenazi; Michal Linial
Journal:  Nucleic Acids Res       Date:  2009-05-08       Impact factor: 16.971

7.  CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures.

Authors:  Hamed Bostan; Naomie Salim; Zeti Azura Hussein; Peter Klappa; Mohd Shahir Shamsir
Journal:  Adv Bioinformatics       Date:  2012-10-10

8.  Protein disulfide topology determination through the fusion of mass spectrometric analysis and sequence-based prediction using Dempster-Shafer theory.

Authors:  Rahul Singh; William Murad
Journal:  BMC Bioinformatics       Date:  2013-01-21       Impact factor: 3.169

Review 9.  Scorpion toxins specific for potassium (K+) channels: a historical overview of peptide bioengineering.

Authors:  Zachary L Bergeron; Jon-Paul Bingham
Journal:  Toxins (Basel)       Date:  2012-11-01       Impact factor: 4.546

10.  Short toxin-like proteins abound in Cnidaria genomes.

Authors:  Yitshak Tirosh; Itai Linial; Manor Askenazi; Michal Linial
Journal:  Toxins (Basel)       Date:  2012-11-16       Impact factor: 4.546
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