Publications by authors named "Kevin Karplus"

27Publications

Analysis of nanopore data using hidden Markov models.

Bioinformatics 2015 Jun 3;31(12):1897-903. Epub 2015 Feb 3.

Nanopore Group, Department of Biomolecular Engineering, University of California Santa Cruz, CA 95064, USA.

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June 2015

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands.

Proc Natl Acad Sci U S A 2013 Nov 28;110(47):18910-5. Epub 2013 Oct 28.

Nanopore Group, Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064.

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November 2013

Complete genome sequence of Pyrobaculum oguniense.

Stand Genomic Sci 2012 Jul 20;6(3):336-45. Epub 2012 Jul 20.

Biomolecular Engineering, University of California., Santa Cruz, California, USA.

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July 2012

Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision.

Nat Biotechnol 2012 Feb 14;30(4):344-8. Epub 2012 Feb 14.

Nanopore Group, Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA.

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February 2012

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.

Mol Syst Biol 2011 Oct 11;7:539. Epub 2011 Oct 11.

School of Medicine and Medical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.

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October 2011

Identification of a chemoreceptor zinc-binding domain common to cytoplasmic bacterial chemoreceptors.

J Bacteriol 2011 Sep 1;193(17):4338-45. Epub 2011 Jul 1.

Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.

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September 2011

Identification of prokaryotic small proteins using a comparative genomic approach.

Bioinformatics 2011 Jul 5;27(13):1765-71. Epub 2011 May 5.

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA.

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July 2011

Improving protein secondary structure prediction using a simple k-mer model.

Bioinformatics 2010 Mar 3;26(5):596-602. Epub 2010 Feb 3.

Department of Computer Science, University of Bristol, Woodland Road, Bristol BS8 1UB, UK.

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March 2010

Applying Undertaker to quality assessment.

Proteins 2009 ;77 Suppl 9:191-5

Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.

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January 2010

SAM-T08, HMM-based protein structure prediction.

Authors:
Kevin Karplus

Nucleic Acids Res 2009 Jul 29;37(Web Server issue):W492-7. Epub 2009 May 29.

Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA.

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July 2009

Pokefind: a novel topological filter for use with protein structure prediction.

Bioinformatics 2009 Jun;25(12):i281-8

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.

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June 2009

Applying undertaker cost functions to model quality assessment.

Proteins 2009 May;75(3):550-5

University of California at Santa Cruz, Biomolecular Engineering, Santa Cruz, CA, USA.

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May 2009

Model quality assessment using distance constraints from alignments.

Proteins 2009 May;75(3):540-9

Department of Computer Science, University of Copenhagen, Copenhagen, Denmark.

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May 2009

PREDICT-2ND: a tool for generalized protein local structure prediction.

Bioinformatics 2008 Nov 30;24(21):2453-9. Epub 2008 Aug 30.

Department of Biomolecular Engineering, University of California, Santa Cruz, CA 95064, USA.

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November 2008

Contact prediction using mutual information and neural nets.

Proteins 2007 ;69 Suppl 8:159-64

Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.

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January 2008

Identification and characterization of RbmA, a novel protein required for the development of rugose colony morphology and biofilm structure in Vibrio cholerae.

J Bacteriol 2006 Feb;188(3):1049-59

Department of Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.

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February 2006

Methods of translating NMR proton distances into their corresponding heavy atom distances for protein structure prediction with limited experimental data.

Protein Eng Des Sel 2005 Dec 24;18(12):597-605. Epub 2005 Oct 24.

PO Box 2548, Sunnyvale, CA 94087-0548 and Department of Biomolecular Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064. USA.

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December 2005

SAM-T04: what is new in protein-structure prediction for CASP6.

Proteins 2005 ;61 Suppl 7:135-42

Biomolecular Engineering Department, University of California, Santa Cruz, California 95064, USA.

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May 2006