PoPS

A computational tool for modeling and predicting protease specificity

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

12 Citations (Scopus)

Abstract

Proteases play a fundamental role in the control of intra- and extracellular processes by binding and cleaving specific amino acid sequences. Identifying these targets is extremely challenging. Current computational attempts to predict cleavage sites are limited, representing these amino acid sequences as patterns or frequency matrices. Here we present PoPS, a publicly accessible bioinformatics tool (http://pops.csse.monash.edu.au/)which provides a novel method for building computational models of protease specificity that, while still being based on these amino acid sequences, can be built from any experimental data or expert knowledge available to the user. PoPS specificity models can be used to predict and rank likely cleavages within a single substrate, and within entire proteomes. Other factors, such as the secondary or tertiary structure of the substrate, can be used to screen unlikely sites. Furthermore, the tool also provides facilities to infer, compare and test models, and to store them in a publicly accessible database.

Original languageEnglish
Title of host publicationProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
PublisherIEEE Computer Society
Pages372-381
Number of pages10
ISBN (Print)0769521940, 9780769521947
Publication statusPublished - 1 Jan 2004
EventProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 - Stanford, CA, United States of America
Duration: 16 Aug 200419 Aug 2004

Conference

ConferenceProceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004
CountryUnited States of America
CityStanford, CA
Period16/08/0419/08/04

Cite this

Boyd, S. E., De La Banda, M. G., Pike, R. N., Whisstock, J. C., & Rudy, G. B. (2004). PoPS: A computational tool for modeling and predicting protease specificity. In Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004 (pp. 372-381). IEEE Computer Society.
Boyd, Sarah E. ; De La Banda, Maria Garcia ; Pike, Robert N. ; Whisstock, James C. ; Rudy, George B. / PoPS : A computational tool for modeling and predicting protease specificity. Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. IEEE Computer Society, 2004. pp. 372-381
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abstract = "Proteases play a fundamental role in the control of intra- and extracellular processes by binding and cleaving specific amino acid sequences. Identifying these targets is extremely challenging. Current computational attempts to predict cleavage sites are limited, representing these amino acid sequences as patterns or frequency matrices. Here we present PoPS, a publicly accessible bioinformatics tool (http://pops.csse.monash.edu.au/)which provides a novel method for building computational models of protease specificity that, while still being based on these amino acid sequences, can be built from any experimental data or expert knowledge available to the user. PoPS specificity models can be used to predict and rank likely cleavages within a single substrate, and within entire proteomes. Other factors, such as the secondary or tertiary structure of the substrate, can be used to screen unlikely sites. Furthermore, the tool also provides facilities to infer, compare and test models, and to store them in a publicly accessible database.",
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Boyd, SE, De La Banda, MG, Pike, RN, Whisstock, JC & Rudy, GB 2004, PoPS: A computational tool for modeling and predicting protease specificity. in Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. IEEE Computer Society, pp. 372-381, Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004, Stanford, CA, United States of America, 16/08/04.

PoPS : A computational tool for modeling and predicting protease specificity. / Boyd, Sarah E.; De La Banda, Maria Garcia; Pike, Robert N.; Whisstock, James C.; Rudy, George B.

Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. IEEE Computer Society, 2004. p. 372-381.

Research output: Chapter in Book/Report/Conference proceedingConference PaperResearchpeer-review

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AB - Proteases play a fundamental role in the control of intra- and extracellular processes by binding and cleaving specific amino acid sequences. Identifying these targets is extremely challenging. Current computational attempts to predict cleavage sites are limited, representing these amino acid sequences as patterns or frequency matrices. Here we present PoPS, a publicly accessible bioinformatics tool (http://pops.csse.monash.edu.au/)which provides a novel method for building computational models of protease specificity that, while still being based on these amino acid sequences, can be built from any experimental data or expert knowledge available to the user. PoPS specificity models can be used to predict and rank likely cleavages within a single substrate, and within entire proteomes. Other factors, such as the secondary or tertiary structure of the substrate, can be used to screen unlikely sites. Furthermore, the tool also provides facilities to infer, compare and test models, and to store them in a publicly accessible database.

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Boyd SE, De La Banda MG, Pike RN, Whisstock JC, Rudy GB. PoPS: A computational tool for modeling and predicting protease specificity. In Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. IEEE Computer Society. 2004. p. 372-381