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The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a systematic approach for sequence-to-structure alignment, called 'KÃSync', in which alignments are generated by dynamic programming using a scoring function that combines information on many protein features, including a novel measure of how obligate a sequence region is to the protein fold. Bydoi:10.1093/nar/gkl480 pmid:16971460 pmcid:PMC1635247 fatcat:s4p75exjqvaf7c4bcefwj7rubq