Kevin Karplus Publications
17 Sept 2008–9 Sept 2011
(Last Update:
15:37 PDT 26 September 2011
)
This page has pointers to papers published between
17 Sept 2008 and 9 Sept 2011.
Refereed Journal Articles
- Jenny Draper, Kevin Karplus, and Karen M. Ottemann.
CZ: A Zinc-binding domain common to cytoplasmic bacterial chemoreceptors.
Journal of Bacteriology (193)17:4338-4345, September 2011.
doi:10.1128/JB.05140-11
- Josue Samayoa, Fitnat Yildiz, and Kevin Karplus
Identification of Prokaryotic Small Proteins using a Comparative Genomic Approach.
Bioinformatics, 27 (13): 1765-1771, 2011.
doi:10.1093/bioinformatics/btr275
-
Martin Madera, Ryan Calmus, Grant Thiltgen, Kevin Karplus, and Julian Gough.
Improving protein secondary structure prediction using a simple k-mer model.
Bioinformatics, 26(5):596–602, March 2010.
doi:10.1093/bioinformatics/btq020
- Elmar Krieger and
Keehyoung Joo and Jinwoo Lee and Jooyoung Lee and
Srivatsan Raman and James Thompson and Mike Tyka and David Baker and
Kevin Karplus.
Improving physical realism, stereochemistry and side-chain accuracy in homology modeling: four approaches that performed well in CASP8.
Proteins: Structure, Function, and Bioinformatics,
77(S9):114–122, 12~August 2009.
CASP8 special issue.
doi:10.1002/prot.22570
- John G. Archie, Martin Paluszewski, and Kevin Karplus.
Applying Undertaker to Quality Assessment.
Proteins: Structure, Function, and Bioinformatics,
77(S9):191–195, 12~August 2009.
CASP8 special issue.
doi10.1002/prot.22508
preprint
- Kevin Karplus.
SAM-T08: HMM-based Protein Structure Prediction.
Nucleic Acids Research 37(Suppl.2):W492-E497, 2009, Web Server
importance of null models in bioinformaticsIssue.
doi:10.1093/nar/gkp403
- Firas Khatib, Carol A. Rohl, and Kevin Karplus.
Pokefind: a novel topological filter for use with protein structure prediction.
Bioinformatics 2009 25(12):i281-i288;
doi:10.1093/bioinformatics/btp198
Refereed Conference Articles
- Rasmus Fonseca, Pawel Winter, and Kevin Karplus.
Protein Packing Quality Using Delaunay Complexes.
In Eighth International Symposium on Voronoi Diagrams in Science and Engineering,
Qingdao, China, June 28th - 30th, 2011.
pdf
Presented by Rasmus Fonseca.
Tech reports and other unrefereed articles
- Blog http://karplus4arduino.wordpress.com
with 26 posts
between 14 June 2011 and 2 Sept 2011 and 670 page views. This blog contains
articles about the Arduino microprocessor board, peripherals for it,
programming, PC board design, robotics, and computer synthesis of music.
- Blog http://gasstationwithoutpumps.wordpress.com with 366
posts between 1 June 2010 and 2 Sept 2011 and over 52,250 page
views. This blog is an eclectic mix containing articles on a
variety of topics, including education, robotics, bioinformatics,
raising gifted children, bicycle transportation, campus planning,
and anything else that attracts my interest.
Recent talks (not complete—just those with slides on-line)
- 1 Aug 2011
- Bioinformatics Methods for COSMOS.
- 20 Nov 2009
- Tech Writing Quick Review
- 1 Oct 2009
- What the Karplus lab does
Presentation about the research in my lab for departmental research
seminar (BME 280B)
- 22 July 2009
- Tutorial on
protein structure prediction
(2 hours for COSMOS)
- 28 May 2009
- Origami with strings: protein folding by computer
(Guest lecture in BME 110 for Todd Lowe)
- 8 May 2009
- Better than chance: the
importance of null models in bioinformatics
University College Dublin (Dublin, Ireland) [note: re-used older set
of slides]
- Dec 2008
- three short talks at CASP8:
Two using Tweaking structures:
working on the fiddly bits
One based on poster Is there any point to
human prediction?
- 28 Oct 2008
- Model Quality Assessment: Guessing how good protein
structure predictions are
Department seminar.
Questions about page content should be directed to
Kevin Karplus
Biomolecular Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064
USA
karplus@soe.ucsc.edu
1-831-459-4250
318 Physical Sciences Building
