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HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Remmert M, Biegert A, Hauser A, Söding J. Remmert M, et al. Among authors: biegert a. Nat Methods. 2011 Dec 25;9(2):173-5. doi: 10.1038/nmeth.1818. Nat Methods. 2011. PMID: 22198341
Discriminative modelling of context-specific amino acid substitution probabilities.
Angermüller C, Biegert A, Söding J. Angermüller C, et al. Among authors: biegert a. Bioinformatics. 2012 Dec 15;28(24):3240-7. doi: 10.1093/bioinformatics/bts622. Epub 2012 Oct 17. Bioinformatics. 2012. PMID: 23080114
HHsenser: exhaustive transitive profile search using HMM-HMM comparison.
Söding J, Remmert M, Biegert A, Lupas AN. Söding J, et al. Among authors: biegert a. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W374-8. doi: 10.1093/nar/gkl195. Nucleic Acids Res. 2006. PMID: 16845029 Free PMC article.
The MPI Bioinformatics Toolkit for protein sequence analysis.
Biegert A, Mayer C, Remmert M, Söding J, Lupas AN. Biegert A, et al. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W335-9. doi: 10.1093/nar/gkl217. Nucleic Acids Res. 2006. PMID: 16845021 Free PMC article.
The Toolkit provides a friendly and intuitive user interface with an online help facility. As a key feature, various tools are interconnected so that the results of one tool can be forwarded to other tools. One could run PSI-BLAST, parse out a multiple alignm …
The Toolkit provides a friendly and intuitive user interface with an online help facility. As a key feature, various tools are …
The HHpred interactive server for protein homology detection and structure prediction.
Söding J, Biegert A, Lupas AN. Söding J, et al. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8. doi: 10.1093/nar/gki408. Nucleic Acids Res. 2005. PMID: 15980461 Free PMC article.
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. ...A detailed help facility is available. As a demonstration, we analyze the s …
It allows to search a wide choice of databases, such as the PDB, SCOP, Pfam, SMART, COGs and CDD. It accepts a single query se …
HHrep: de novo protein repeat detection and the origin of TIM barrels.
Söding J, Remmert M, Biegert A. Söding J, et al. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W137-42. doi: 10.1093/nar/gkl130. Nucleic Acids Res. 2006. PMID: 16844977 Free PMC article.
HHrep is a web server for the de novo identification of repeats in protein sequences, which is based on the pairwise comparison of profile hidden Markov models (HMMs). ...We illustrate this with proteins from four superfamilies of TIM barrels by revealing a clear 4- …
HHrep is a web server for the de novo identification of repeats in protein sequences, which is based on the pairwise comparison of pr …
Fast and accurate automatic structure prediction with HHpred.
Hildebrand A, Remmert M, Biegert A, Söding J. Hildebrand A, et al. Among authors: biegert a. Proteins. 2009;77 Suppl 9:128-32. doi: 10.1002/prot.22499. Proteins. 2009. PMID: 19626712
Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin.
Remmert M, Biegert A, Linke D, Lupas AN, Söding J. Remmert M, et al. Among authors: biegert a. Mol Biol Evol. 2010 Jun;27(6):1348-58. doi: 10.1093/molbev/msq017. Epub 2010 Jan 27. Mol Biol Evol. 2010. PMID: 20106904
Sequence context-specific profiles for homology searching.
Biegert A, Söding J. Biegert A, et al. Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3770-5. doi: 10.1073/pnas.0810767106. Epub 2009 Feb 20. Proc Natl Acad Sci U S A. 2009. PMID: 19234132 Free PMC article.
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