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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.
Protein homology detection by HMM-HMM comparison.
Söding J. Söding J. Bioinformatics. 2005 Apr 1;21(7):951-60. doi: 10.1093/bioinformatics/bti125. Epub 2004 Nov 5. Bioinformatics. 2005. PMID: 15531603
Retroactive, a membrane-anchored extracellular protein related to vertebrate snake neurotoxin-like proteins, is required for cuticle organization in the larva of Drosophila melanogaster.
Moussian B, Söding J, Schwarz H, Nüsslein-Volhard C. Moussian B, et al. Dev Dyn. 2005 Jul;233(3):1056-63. doi: 10.1002/dvdy.20389. Dev Dyn. 2005. PMID: 15844167
REPPER--repeats and their periodicities in fibrous proteins.
Gruber M, Söding J, Lupas AN. Gruber M, et al. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W239-43. doi: 10.1093/nar/gki405. Nucleic Acids Res. 2005. PMID: 15980460 Free PMC article.
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.
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.
HHsenser: exhaustive transitive profile search using HMM-HMM comparison.
Söding J, Remmert M, Biegert A, Lupas AN. Söding J, et al. 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.
Comparative analysis of coiled-coil prediction methods.
Gruber M, Söding J, Lupas AN. Gruber M, et al. J Struct Biol. 2006 Aug;155(2):140-5. doi: 10.1016/j.jsb.2006.03.009. Epub 2006 Mar 31. J Struct Biol. 2006. PMID: 16870472
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