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). It allows to search a wide choice of databases, such as the PDB, SCOP, Pfam, SMART, COGs and CDD. It accepts a single query sequence or a multiple alignment as input. Within only a few minutes it returns the search results in a user-friendly format similar to that of PSI-BLAST. Search options include local or global alignment and scoring secondary structure similarity. HHpred can produce pairwise query-template alignments, multiple alignments of the query with a set of templates selected from the search results, as well as 3D structural models that are calculated by the MODELLER software from these alignments. A detailed help facility is available. As a demonstration, we analyze the sequence of SpoVT, a transcriptional regulator from Bacillus subtilis. HHpred can be accessed at http://protevo.eb.tuebingen.mpg.de/hhpred.

References in zbMATH (referenced in 7 articles )

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  1. Wong, Samuel W. K.; Liu, Jun S.; Kou, S. C.: Exploring the conformational space for protein folding with sequential Monte Carlo (2018)
  2. Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
  3. Kasabov, Nikola (ed.): Springer handbook of bio-/neuro-informatics (2014)
  4. Xiong, Bing; Wu, Jie; Burk, David L.; Xue, Mengzhu; Jiang, Hualiang; Shen, Jingkang: BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server (2010) ioport
  5. Petrossian, Tanya C.; Clarke, Steven G.: Computational methods to identify novel methyltransferases (2009) ioport
  6. Kaján, László; Rychlewski, Leszek: Evaluation of 3D-jury on CASP7 models (2007) ioport
  7. Söding, Johannes; Biegert, Andreas; Lupas, Andrei N.: The hhpred interactive server for protein homology detection and structure prediction. (2005) ioport