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Open Access Software

Distill: a suite of web servers for the prediction of one-, two- and three-dimensional structural features of proteins

Davide Baú, Alberto JM Martin, Catherine Mooney, Alessandro Vullo, Ian Walsh and Gianluca Pollastri*

Author Affiliations

School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland

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BMC Bioinformatics 2006, 7:402  doi:10.1186/1471-2105-7-402

Published: 5 September 2006

Abstract

Background

We describe Distill, a suite of servers for the prediction of protein structural features: secondary structure; relative solvent accessibility; contact density; backbone structural motifs; residue contact maps at 6, 8 and 12 Angstrom; coarse protein topology. The servers are based on large-scale ensembles of recursive neural networks and trained on large, up-to-date, non-redundant subsets of the Protein Data Bank. Together with structural feature predictions, Distill includes a server for prediction of Cα traces for short proteins (up to 200 amino acids).

Results

The servers are state-of-the-art, with secondary structure predicted correctly for nearly 80% of residues (currently the top performance on EVA), 2-class solvent accessibility nearly 80% correct, and contact maps exceeding 50% precision on the top non-diagonal contacts. A preliminary implementation of the predictor of protein Cα traces featured among the top 20 Novel Fold predictors at the last CASP6 experiment as group Distill (ID 0348). The majority of the servers, including the Cα trace predictor, now take into account homology information from the PDB, when available, resulting in greatly improved reliability.

Conclusion

All predictions are freely available through a simple joint web interface and the results are returned by email. In a single submission the user can send protein sequences for a total of up to 32k residues to all or a selection of the servers. Distill is accessible at the address: http://distill.ucd.ie/distill/ webcite.