Protein function annotation by homology-based inference 英文参考文献.docVIP

Review Protein function annotation by homology-based inference Yaniv Loewenstein*, Domenico Raimondo?, Oliver C Redfern?, James Watson§, Dmitrij Frishman?￥, Michal Linial*, Christine Orengo?, Janet Thornton§ and Anna Tramontano?# Addresses: *Department of Biological Chemistry, The Hebrew University of Jerusalem, Sudarsky Center, Jerusalem 91904, Israel. ?Department of Biochemical Sciences, University of Rome “La Sapienza”, Rome 00185, Italy. ?Research Department of Structural and Molecular Biology, University College, London WC1E, UK. §European Bioinformatics Institute, Hinxton CB10 1SD, UK. ?Technische Universit?t, Munich, Germany. ￥Helmholtz Zentrum, German Research Center for Environmental Health, Munich 85764, Germany. #Pasteur Institute-Cenci Bolognetti Foundation, University of Rome “La Sapienza”, Rome 00185, Italy. Correspondence: Anna Tramontano. Email: anna.tramontano@uniroma1.it Published: 2 February 2009 Genome Biology 2009, 10:207 (doi:10.1186/gb-2009-10-2-207) The electronic version of this article is the complete one and can be found online at /2009/10/2/207 ? 2009 BioMed Central Ltd Abstract With many genomes now sequenced, computational annotation methods to characterize genes and proteins from their sequence are increasingly important. The BioSapiens Network has developed tools to address all stages of this process, and here we review progress in the automated prediction of protein function based on protein sequence and structure. In the past, a protein’s structure was usually experimentally determined after its biological role had been thoroughly elucidated, and the structure was used as a framework to explain known functional properties. This led to the view that the reliable prediction of the structure of a protein from its sequence would almost automatically provide infor- mation about its function. The good news is that methods for predicting structure from sequen