CysView: Protein classification based on cysteine pairing patterns

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

doi:10.1093/nar/gkh475

CysView: Protein classification based on cysteine pairing patterns

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

Research output: Journal Publication › Article › peer-review

21 Citations (Scopus)

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/.

Original language	English
Pages (from-to)	W350-W355
Journal	Nucleic Acids Research
Volume	32
Issue number	WEB SERVER ISS.
DOIs	https://doi.org/10.1093/nar/gkh475
Publication status	Published - 1 Jul 2004
Externally published	Yes

ASJC Scopus subject areas

Genetics

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title = "CysView: Protein classification based on cysteine pairing patterns",

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/.",

author = "Johann Lenffer and Paulo Lai and {El Mejaber}, Wafaa and Khan, {Asif M.} and Koh, {Judice L.Y.} and Tan, {Paul T.J.} and Seah, {Seng H.} and Vladimir Brusic",

note = "Funding Information: The authors would like to thank K. N. Srinivasan and two anonymous reviewers for their useful comments on the manuscript. J.L., P.L. and W.E.M. were international exchange students supported by the Institute for Infocomm Research, Singapore. A.M.K. and P.T.J.T. are graduate student scholars at the National University of Singapore.",

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doi = "10.1093/nar/gkh475",

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AU - Lenffer, Johann

AU - Lai, Paulo

AU - El Mejaber, Wafaa

AU - Khan, Asif M.

AU - Koh, Judice L.Y.

AU - Tan, Paul T.J.

AU - Seah, Seng H.

AU - Brusic, Vladimir

N1 - Funding Information: The authors would like to thank K. N. Srinivasan and two anonymous reviewers for their useful comments on the manuscript. J.L., P.L. and W.E.M. were international exchange students supported by the Institute for Infocomm Research, Singapore. A.M.K. and P.T.J.T. are graduate student scholars at the National University of Singapore.

PY - 2004/7/1

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AB - 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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CysView: Protein classification based on cysteine pairing patterns

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ASJC Scopus subject areas

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