HH-suite

The HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. These sequence searches are a standard tool in modern biology with which the function of unknown proteins can be inferred from their sequence.

HHsearch takes as input a multiple sequence alignment or a profile hidden Markov Model (HMM) and searches a database of profile HMMs for homologous (related) proteins. HHsearch is often used for homology modeling, that is, to build a model of the structure of a query protein for which only the sequence is known: For that purpose, a database of proteins with known structures such as the protein data bank is searched for "template" proteins similar to the query protein. If such a template protein is found, the structure of the protein of interest can be predicted based on a pairwise sequence alignment of the query with the template protein sequence. In the CASP9 protein structure prediction competition in 2010, a fully automated version of HHpred based on HHsearch and HHblits was ranked best out of 81 servers in template-based structure prediction CASP9 TBM/FM.