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Bioinformatics Advance Access published online on September 16, 2008
Bioinformatics, 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 1 and Silvio C.E. Tosatto 1,*

1Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy

*To whom correspondence should be addressed. Prof. Silvio Tosatto, E-mail: silvio{at}cribi.unipd.it, silvio.tosatto{at}unipd.it


  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; (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 less than 2.0 A. 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/.

Associate Editor: Prof. Burkhard Rost

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

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