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Söding, J, Biegert, A and Lupas, AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33:W244-8
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.
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
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