Motif-based fold assignment.

Conventional fold recognition techniques rely mainly on the analysis of the entire sequence of a protein. We present an MBA method to improve performance of any conventional sequence-based fold assignment. The method uses sequence motifs, such as those defined in the Prosite database, and the SwissProt annotation of the fold library. When combined with a simple SDP method, the coverage of MBA is comparable to the results obtained with PSI-BLAST. However, the set of the MBA predictions is significantly different from that of PSI-BLAST, leading to a 40% increase of the coverage for the combined MBA/PSI-BLAST method. The MBA approach can be easily adopted to include the results of sequence-independent function prediction methods and alternative motif and annotation databases. The method is available through the web server localized at http://www.doe-mbi.ucla.edu/mba.