<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Espadaler, J.</style></author><author><style face="normal" font="default" size="100%">Eswar, N.</style></author><author><style face="normal" font="default" size="100%">Querol, E.</style></author><author><style face="normal" font="default" size="100%">Aviles, F. X.</style></author><author><style face="normal" font="default" size="100%">Sali, A.</style></author><author><style face="normal" font="default" size="100%">M. A. Marti-Renom</style></author><author><style face="normal" font="default" size="100%">Oliva, B.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Prediction of enzyme function by combining sequence similarity and protein interactions</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Bioinformatics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Amino Acid *Software Structure-Activity Relationship Substrate Specificity/genetics</style></keyword><keyword><style  face="normal" font="default" size="100%">Amino Acid Sequence/physiology Databases</style></keyword><keyword><style  face="normal" font="default" size="100%">Automated Predictive Value of Tests Protein Interaction Mapping Proteins/analysis/metabolism Sequence Alignment Sequence Analysis</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein *Sequence Homology</style></keyword><keyword><style  face="normal" font="default" size="100%">Protein Enzymes/analysis/*metabolism Fuzzy Logic Pattern Recognition</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=18505562</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">249</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: 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.</style></abstract><notes><style face="normal" font="default" size="100%">Espadaler, Jordi Eswar, Narayanan Querol, Enrique Aviles, Francesc X Sali, Andrej Marti-Renom, Marc A Oliva, Baldomero GM54762/GM/NIGMS NIH HHS/United States GM71790/GM/NIGMS NIH HHS/United States GM74929/GM/NIGMS NIH HHS/United States GM74945/GM/NIGMS NIH HHS/United States Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t England BMC bioinformatics BMC Bioinformatics. 2008 May 27;9:249.</style></notes></record></records></xml>