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Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.
Gough J, Karplus K, Hughey R, Chothia C. Gough J, et al. Among authors: karplus k. J Mol Biol. 2001 Nov 2;313(4):903-19. doi: 10.1006/jmbi.2001.5080. J Mol Biol. 2001. PMID: 11697912
CAFASP-1: critical assessment of fully automated structure prediction methods.
Fischer D, Barret C, Bryson K, Elofsson A, Godzik A, Jones D, Karplus KJ, Kelley LA, MacCallum RM, Pawowski K, Rost B, Rychlewski L, Sternberg M. Fischer D, et al. Among authors: karplus kj. Proteins. 1999;Suppl 3:209-17. doi: 10.1002/(sici)1097-0134(1999)37:3+<209::aid-prot27>3.3.co;2-p. Proteins. 1999. PMID: 10526371
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Sievers F, et al. Among authors: karplus k. Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75. Mol Syst Biol. 2011. PMID: 21988835 Free PMC article.
Improving protein secondary structure prediction using a simple k-mer model.
Madera M, Calmus R, Thiltgen G, Karplus K, Gough J. Madera M, et al. Among authors: karplus k. Bioinformatics. 2010 Mar 1;26(5):596-602. doi: 10.1093/bioinformatics/btq020. Epub 2010 Feb 3. Bioinformatics. 2010. PMID: 20130034 Free PMC article.
Calibrating E-values for hidden Markov models using reverse-sequence null models.
Karplus K, Karchin R, Shackelford G, Hughey R. Karplus K, et al. Bioinformatics. 2005 Nov 15;21(22):4107-15. doi: 10.1093/bioinformatics/bti629. Epub 2005 Aug 25. Bioinformatics. 2005. PMID: 16123115
Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.
Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K. Karchin R, et al. Among authors: karplus k. Proteins. 2003 Jun 1;51(4):504-14. doi: 10.1002/prot.10369. Proteins. 2003. PMID: 12784210
SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome.
Dolinsky TJ, Burgers PM, Karplus K, Baker NA. Dolinsky TJ, et al. Among authors: karplus k. Bioinformatics. 2004 Sep 22;20(14):2312-4. doi: 10.1093/bioinformatics/bth223. Epub 2004 Apr 1. Bioinformatics. 2004. PMID: 15059824
Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods.
Park J, Karplus K, Barrett C, Hughey R, Haussler D, Hubbard T, Chothia C. Park J, et al. Among authors: karplus k. J Mol Biol. 1998 Dec 11;284(4):1201-10. doi: 10.1006/jmbi.1998.2221. J Mol Biol. 1998. PMID: 9837738
Hidden Markov models for detecting remote protein homologies.
Karplus K, Barrett C, Hughey R. Karplus K, et al. Bioinformatics. 1998;14(10):846-56. doi: 10.1093/bioinformatics/14.10.846. Bioinformatics. 1998. PMID: 9927713
AVAILABILITY: A World Wide Web server, as well as information on obtaining the Sequence Alignment and Modeling (SAM) software suite, can be found at http://www.cse.ucsc.edu/research/compbi o/ CONTACT: karplus@cse.ucsc.edu; http://www.cse.ucsc.edu/karplus...
AVAILABILITY: A World Wide Web server, as well as information on obtaining the Sequence Alignment and Modeling (SAM) software suite, can be …
Scoring hidden Markov models.
Barrett C, Hughey R, Karplus K. Barrett C, et al. Among authors: karplus k. Comput Appl Biosci. 1997 Apr;13(2):191-9. doi: 10.1093/bioinformatics/13.2.191. Comput Appl Biosci. 1997. PMID: 9146967
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