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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...

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Detalles Bibliográficos
Autores principales: Söding, Johannes, Biegert, Andreas, Lupas, Andrei N.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160169/
https://www.ncbi.nlm.nih.gov/pubmed/15980461
http://dx.doi.org/10.1093/nar/gki408
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author Söding, Johannes
Biegert, Andreas
Lupas, Andrei N.
author_facet Söding, Johannes
Biegert, Andreas
Lupas, Andrei N.
author_sort Söding, Johannes
collection PubMed
description 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 .
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spelling pubmed-11601692005-06-29 The HHpred interactive server for protein homology detection and structure prediction Söding, Johannes Biegert, Andreas Lupas, Andrei N. Nucleic Acids Res Article 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 . Oxford University Press 2005-07-01 2005-06-27 /pmc/articles/PMC1160169/ /pubmed/15980461 http://dx.doi.org/10.1093/nar/gki408 Text en © The Author 2005. Published by Oxford University Press. All rights reserved
spellingShingle Article
Söding, Johannes
Biegert, Andreas
Lupas, Andrei N.
The HHpred interactive server for protein homology detection and structure prediction
title The HHpred interactive server for protein homology detection and structure prediction
title_full The HHpred interactive server for protein homology detection and structure prediction
title_fullStr The HHpred interactive server for protein homology detection and structure prediction
title_full_unstemmed The HHpred interactive server for protein homology detection and structure prediction
title_short The HHpred interactive server for protein homology detection and structure prediction
title_sort hhpred interactive server for protein homology detection and structure prediction
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160169/
https://www.ncbi.nlm.nih.gov/pubmed/15980461
http://dx.doi.org/10.1093/nar/gki408
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