HHsearch is a software suite for detecting remote homologues of proteins and generating highquality alignments for homology modeling and function prediction. HHsearch’s performance is testified by the fact that a fully automated version HHpred2 is ranked second best automatic server in the CASP7 blind structure prediction benchmark (2006) while being about > 50 times faster than the other top 20 servers.
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Protein homology detection by HMM–HMM comparison
Bioinformatics (2005) 21 (7): 951-960