Peptides

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Full results for the classification of 182 Enzyme Commission (EC) classes, using Peptidic Programs can be found here.

  • These are the full datasets used (82 MB).
  • The source code used for the classifier is available here under the GPL license.


A more specialized version of the program for detailed classification of the last digit of EC classes is presented here


Research Team


Publications

BibTeX source
Hermann Pimentel Schuenemann, Computação Paralela na Classificação de Proteínas sobre a Plataforma CellBE Master Thesis, Universidade de Lisboa - Faculdade de Ciências - Departamento de Informática, Nov 2010.

| Presentation | BibTeX source
Andre O Falcao, Daniel Faria, Antonio Ferreira, Peptide programs: applying fragment programs to protein classification.Proceedings of the CIKM 2008 - DTMBio 2008 Workshop November, 2008.

DOI | | BibTeX source
Daniel Faria, António EN Ferreira, Andre O Falcao 2009: Enzyme classification with peptide programs: a comparative study. BMC Bioinformatics (10), 231.

BibTeX source
Andre O Falcao, Daniel Faria, Antonio Ferreira, Peptide Programs: Applying Fragment Programs to Protein Classification.DTMBIO'08 : Proceedings of the 2008 ACM 2nd CIKM workshop on Data and Text Mining Methods in Bioinformatics New York, NY, USA, October, in press. ACM.

BibTeX source
Andre O Falcao, Residue Fragment Programs for Enzyme Classification. Em: Francisco Couto, Mário J. Silva, Pedro Fernandes (Eds.), Proceedings of BKDB2005 -- Bioinformatics: knowledge discovery in biology p. 24-28, June, 2005.

DOI | | BibTeX source
Catia Pesquita, Daniel Faria, Hugo Bastos, António Ferreira, Andre O Falcao, Francisco Couto 2008: Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinformatics Suppl 5(9), S4.

DOI | | BibTeX source
Hugo Bastos, Daniel Faria, Catia Pesquita, Andre O. Falcao, BOLOS: BLAST Ontology-Linked hOmologue Stars.SAC '08: Proceedings of the 2008 ACM symposium on Applied computing New York, NY, USA, March, 2008. ACM.

BibTeX source
Hugo Bastos, Clustering algorithms for improving protein functional classification techniques Master Thesis, University of Lisbon, Faculty of Sciences, February 2008.

BibTeX source
Hugo Bastos, Daniel Faria, Catia Pesquita, Andre O. Falcao, Using GO terms to evaluate protein clustering.BioOntologies SIG at ISMB/ECCB - 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) July, 2007.


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