PMID:15980461: Difference between revisions

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Citation	No author listed (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33:W244-8
Abstract	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.
Links	PubMed PMC1160169 Online version:10.1093/nar/gki408
Keywords	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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Gene product	Qualifier	GO ID	GO term name	Evidence Code	with/from	Aspect	Notes	Status
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HHpred
Category:Bioinformatics_Tools

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-<span style = 'font-size: large'> '''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</span>
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-|{{TableHeadingColor}} |'''Abstract''' || 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.
+!align=left  |Citation
-</noinclude>
+||
+'''No author listed'''  (2005) The HHpred interactive server for protein homology detection and structure prediction. ''Nucleic Acids Res.'' '''33''':W244-8
+|-
+!align=left  |Abstract
+||
+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.
+|-
+!align=left  |Links
+||
+[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15980461 PubMed] [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160169 PMC1160169]
+Online version:[http://dx.doi.org/10.1093/nar/gki408 10.1093/nar/gki408]
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-|{{TableHeadingColor}} nowrap |'''Links''' ||  [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15980461 PubMed]
+!align=left  |Keywords
+||
+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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