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Detection of internal repeats: how common are they?
Heringa J. Heringa J. Curr Opin Struct Biol. 1998 Jun;8(3):338-45. doi: 10.1016/s0959-440x(98)80068-7. Curr Opin Struct Biol. 1998. PMID: 9666330 Review.
Global multiple-sequence alignment with repeats.
Sammeth M, Heringa J. Sammeth M, et al. Among authors: heringa j. Proteins. 2006 Jul 1;64(1):263-74. doi: 10.1002/prot.20957. Proteins. 2006. PMID: 16609972
Computational methods for protein secondary structure prediction using multiple sequence alignments.
Heringa J. Heringa J. Curr Protein Pept Sci. 2000 Nov;1(3):273-301. doi: 10.2174/1389203003381324. Curr Protein Pept Sci. 2000. PMID: 12369910 Review.
Integrating protein secondary structure prediction and multiple sequence alignment.
Simossis VA, Heringa J. Simossis VA, et al. Among authors: heringa j. Curr Protein Pept Sci. 2004 Aug;5(4):249-66. doi: 10.2174/1389203043379675. Curr Protein Pept Sci. 2004. PMID: 15320732 Review.
Strain in protein structures as viewed through nonrotameric side chains: I. their position and interaction.
Heringa J, Argos P. Heringa J, et al. Proteins. 1999 Oct 1;37(1):30-43. Proteins. 1999. PMID: 10451548
The evolution and recognition of protein sequence repeats.
Heringa J. Heringa J. Comput Chem. 1994 Sep;18(3):233-43. doi: 10.1016/0097-8485(94)85018-6. Comput Chem. 1994. PMID: 7952894
Side-chain clusters in protein structures and their role in protein folding.
Heringa J, Argos P. Heringa J, et al. J Mol Biol. 1991 Jul 5;220(1):151-71. doi: 10.1016/0022-2836(91)90388-m. J Mol Biol. 1991. PMID: 2067014
The REPRO server: finding protein internal sequence repeats through the Web.
George RA, Heringa J. George RA, et al. Among authors: heringa j. Trends Biochem Sci. 2000 Oct;25(10):515-7. doi: 10.1016/s0968-0004(00)01643-1. Trends Biochem Sci. 2000. PMID: 11203383 No abstract available.
Strain in protein structures as viewed through nonrotameric side chains: II. effects upon ligand binding.
Heringa J, Argos P. Heringa J, et al. Proteins. 1999 Oct 1;37(1):44-55. Proteins. 1999. PMID: 10451549
Three-dimensional domain duplication, swapping and stealing.
Heringa J, Taylor WR. Heringa J, et al. Curr Opin Struct Biol. 1997 Jun;7(3):416-21. doi: 10.1016/s0959-440x(97)80060-7. Curr Opin Struct Biol. 1997. PMID: 9204285 Review.
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