I recently came across HHpred
(described in Soding et al 2005
), a program for looking for remote homologues by using HMMs. A nice use case of this is in the paper by Valentim et al 2013
, where they used HHpred to predict that the Schistosoma mansoni
protein that is involved in response to the drug oxamniquine has structural similarity to sulfotransferases.
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