02031nas a2200253   4500008004100000245009200041210006900133300000800202490000600210520096700216653008801183653004501271653013401316653003101450653007301481100001801554700001401572700001501586700001901601700001301620700002401633700001401657856010601671       2008                        eng d00aPrediction of enzyme function by combining sequence similarity and protein interactions0 aPrediction of enzyme function by combining sequence similarity a  a2490 v93 aBACKGROUND: A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein sequences are more likely to perform the same function if they share similar interacting partners. RESULTS: The method has been tested against the PSI-BLAST program using a set of 3,890 protein sequences from which interaction data was available. For protein sequences that align with at least 40% sequence identity to a known enzyme, the specificity of our method in predicting the first three EC digits increased from 80% to 90% at 80% coverage when compared to PSI-BLAST. CONCLUSION: Our method can also be used in proteins for which homologous sequences with known interacting partners can be detected. Thus, our method could increase 10% the specificity of genome-wide enzyme predictions based on sequence matching by PSI-BLAST alone.10aAmino Acid *Software Structure-Activity Relationship Substrate Specificity/genetics10aAmino Acid Sequence/physiology Databases10aAutomated Predictive Value of Tests Protein Interaction Mapping Proteins/analysis/metabolism Sequence Alignment Sequence Analysis10aProtein *Sequence Homology10aProtein Enzymes/analysis/*metabolism Fuzzy Logic Pattern Recognition1 aEspadaler, J.1 aEswar, N.1 aQuerol, E.1 aAviles, F., X.1 aSali, A.1 aMarti-Renom, M., A.1 aOliva, B.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18505562