Bottom - Index of papers - Paper in HTML - Abstract - Appendix - CUBIC - RostGroup
| Title: | PROFcon: novel prediction of long-range contacts |
| Author: | Marco Punta & Burkhard Rost |
| Quote: | Bioinformatics, 2005, 21:2960-2968 |
Motivation: Despite the continuing advance in the experimental determination of protein structures, the gap betweenthe 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 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, i.e. on families with few homologues. 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@cubic.bioc.columbia.edu
Top -
Index of papers -
Paper in HTML -
Abstract -
Appendix -
CUBIC -
RostGroup