Bioinformatics Advance Access originally published online on May 12, 2005
Bioinformatics 2005 21(13):2960-2968; doi:10.1093/bioinformatics/bti454
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PROFcon: novel prediction of long-range contacts
1CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University 650 West 168th Street BB217, New York, NY 10032, USA
2NorthEast Structural Genomics Consortium (NESG), Department of Biochemistry and Molecular Biophysics, Columbia University 650 West 168th Street BB217, New York, NY 10032, USA
3Columbia University Center for Computational Biology and Bioinformatics (C2B2) Russ Berrie Pavilion, 1150 Street Nicholas Avenue, New York, NY 10032, USA
*To whom correspondence should be addressed.
Motivation: Despite the continuing advance in the experimental determination of protein structures, the gap between the number of known protein sequences and structures continues to increase. Prediction methods can bridge this sequence–structure gap only partially. Better predictions of non-local contacts between residues could improve comparative modeling, fold recognition and could assist in the experimental structure determination.
Results: Here, we introduced PROFcon, a novel contact prediction method that combines information from alignments, from predictions of secondary structure and solvent accessibility, from the region between two residues and from the average properties of the entire protein. In contrast to some other methods, PROFcon predicted short and long proteins at similar levels of accuracy. As expected, PROFcon was clearly less accurate when tested on sparse evolutionary profiles, that is, on families with few homologs. Prediction accuracy was highest for proteins belonging to the SCOP alpha/beta class. PROFcon compared favorably with state-of-the-art prediction methods at the CASP6 meeting. While the performance may still be perceived as low, our method clearly pushed the mark higher. Furthermore, predictions are already accurate enough to seed predictions of global features of protein structure.
Availability: http://www.predictprotein.org/submit_profcon.html
Contact: punta{at}cubic.bioc.columbia.edu
Supplementary information: http://www.rostlab.org/results/2005/profcon
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