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Protein Engineering vol. 16 no. 7 pp. 459-462, 2003
© 2003 Oxford University Press

Simple consensus procedures are effective and sufficient in secondary structure prediction

Mario Albrecht1,3, Silvio C.E. Tosatto2,3, Thomas Lengauer1 and Giorgio Valle2

1Max-Planck-Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany and 2CRIBI Biotechnology Center, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy M.Albrecht and S.C.E.Tosatto contributed equally to this work.

3 To whom correspondence should be addressed. e-mail: mario.albrecht{at}mpi-sb.mpg.de; silvio{at}cribi.unipd.it

We have analyzed the performance of majority voting on minimal combination sets of three state-of-the-art secondary structure prediction methods in order to obtain a consensus prediction. Using three large benchmark sets from the EVA server, our results show a significant improvement in the average Q3 prediction accuracy of up to 1.5 percentage points by consensus formation. The application of an additional trivial filtering procedure for predicted secondary structure elements that are too short, does not significantly affect the prediction accuracy. Our analysis also provides valuable insight into the similarity of the results of the prediction methods that we combine as well as the higher confidence in consistently predicted secondary structure.

Received March 7, 2003; revised May 24, 2003; accepted June 6, 2003.


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