The HHpred interactive server for protein homology detection and structure prediction

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8. doi: 10.1093/nar/gki408.


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

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Databases, Protein
  • Internet
  • Markov Chains
  • Protein Conformation*
  • Sequence Alignment
  • Sequence Analysis, Protein / methods
  • Sequence Homology, Amino Acid*
  • Software*
  • Transcription Factors / chemistry
  • User-Computer Interface


  • Bacterial Proteins
  • Transcription Factors