HHpred is a "fast server for remote protein homology detection and structure prediction and is the first to implement pairwise comparison of profile hidden Markov models (HMMs)".[1]
It provides "sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling".[2]
References[]
- ↑ Söding, Johannes, Andreas Biegert, and Andrei N. Lupas. "The HHpred Interactive Server for Protein Homology Detection and Structure Prediction." Nucleic Acids Research 33.Web Server issue (2005): W244–W248. PMC. Web. 5 June 2015.
- ↑ "Search Tools." Bioinformatics Toolkit. Department of Protein Evolution at the Max Planck Institute for Developmental Biology, Tübingen, 2015. Web. 05 June 2015.