The HHpred interactive server for protein homology detection and structure prediction.
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.
Söding
Johannes
J
Department of Protein Evolution, Max-Planck-Institute for Developmental Biology Spemannstrasse 35, 72076 Tübingen, Germany. johannes.soeding@tuebingen.mpg.de
Biegert
Andreas
A
Lupas
Andrei N
AN
D001426:Bacterial Proteins / Q000737:chemistry; D030562:Databases, Protein; D020407:Internet; D008390:Markov Chains; D011487:Protein Conformation; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods; D017386:Sequence Homology, Amino Acid; D012984:Software; D014157:Transcription Factors / Q000737:chemistry; D014584:User-Computer Interface
D001426:Bacterial Proteins; D014157:Transcription Factors