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Bioinformatics Advance Access originally published online on September 16, 2008
Bioinformatics 2008 24(22):2632-2633; doi:10.1093/bioinformatics/btn488
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

TESE: generating specific protein structure test set ensembles

Francesco Sirocco and Silvio C. E. Tosatto *

Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy

*To whom correspondence should be addressed.


  Abstract

Summary: TESE is a web server for the generation of test sets of protein sequences and structures fulfilling a number of different criteria. At least three different use cases can be envisaged: (i) benchmarking of novel methods; (ii) test sets tailored for special needs and (iii) extending available datasets. The CATH structure classification is used to control structural/sequence redundancy and a variety of structural quality parameters can be used to interactively select protein subsets with specific characteristics, e.g. all X-ray structures of {alpha}-helical repeat proteins with more than 120 residues and resolution <2.0 Å. The output includes FASTA-formatted sequences, PDB files and a clickable HTML index file containing images of the selected proteins. Multiple subsets for cross-validation are also supported.

Availability: The TESE server is available for non-commercial use at URL: http://protein.bio.unipd.it/tese/.

Contact: silvio.tosatto{at}unipd.it

Associate Editor: Burkhard Rost

Received on June 5, 2008; revised on August 26, 2008; accepted on September 10, 2008

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L. Marsella, F. Sirocco, A. Trovato, F. Seno, and S. C.E. Tosatto
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[Abstract] [Full Text] [PDF]


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