PROFcon: novel prediction of long-range contacts. 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:

References in zbMATH (referenced in 5 articles )

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  1. Duarte, Jose M.; Sathyapriya, Rajagopal; Stehr, Henning; Filippis, Ioannis; Lappe, Michael: Optimal contact definition for reconstruction of contact maps (2010) ioport
  2. Xi, Lili; Li, Shuyan; Liu, Huanxiang; Li, Jiazhong; Lei, Beilei; Yao, Xiaojun: Global and local prediction of protein folding rates based on sequence autocorrelation information (2010)
  3. Stout, Michael; Bacardit, Jaume; Hirst, Jonathan D.; Smith, Robert E.; Krasnogor, Natalio: Prediction of topological contacts in proteins using learning classifier systems (2009) ioport
  4. Taylor, William R.: Protein knots and fold complexity: some new twists (2007)
  5. Glasgow, Janice; Kuo, Tony; Davies, Jim: Protein structure from contact maps: A case-based reasoning approach (2006) ioport