A strategy for functionally annotating protein sequences using sequence and predicted structural information is proposed. First, structural models are built using standard, web-based tools. The models are then annotated using the sequence and structure-based annotation method SeSAW, and the structure based ligand. binding site alignment method GIRAF Annotations for several sequences (ATPase-like domains 1 and 2 from mouse RIG-I, the TIR domain from mouse Toll-like receptor 9, and alternative oxidase from Blastocystis) are made and compared with known functional information. We find that the annotations in general make functional sense and provide more specific information than would be available from a purely sequence-based approach.
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