Motivation: Current approaches to contact map prediction in proteins have focused on amino acid conservation and patterns of mutation at sequentially distant positions. This sequence information is poorly understood and very little progress has been made in this area during recent years.

Results: In this study, an observation of ‘striped’ sequence patterns across β-sheets prompted the development of a new type of contact map predictor. Computer program code was evolved with an evolutionary algorithm (genetic programming) to select residues and residue pairs likely to make contacts based solely on local sequence patterns extracted with the help of self-organizing maps. The mean prediction accuracy is 27% on a validation set of 156 domains up to 400 residues in length, where contacts are separated by at least 8 residues and length/10 pairs are predicted. The retrospective accuracy on a set of 15 CASP5 targets is 27% and 14% for length/10 and length/2 predicted pairs, respectively (both using a minimum residue separation of 24). This compares favourably to the equivalent 21% and 13% obtained for the best automated contact prediction methods at CASP5. The results suggest that protein architectures impose regularities in local sequence environments. Other sources of information, such as correlated/compensatory mutations, may further improve accuracy.

Availability: A web-based prediction service is available at http://www.sbc.su.se/~maccallr/contactmaps