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One of the major goals of molecular and evolutionary biology is to understand the functions of proteins by extracting functional information from protein sequences, structures and interactions. In this review, we summarize the repertoire of methods currently being applied and report recent progress in the field of in silico annotation of protein function based on the accumulation of vast amounts of sequence and structure data. In particular, we emphasize the newly developed structure-baseddoi:10.1007/s00726-008-0088-8 pmid:18421562 fatcat:micrifjcrfetnafnm4fx45ouom