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.