Kevin Karplus's Lab group publications

This web page is for publications of Kevin Karplus's group in protein-structure prediction (and, eventually, protein design). Although this list of papers is fairly complete, the links to online copies are mostly not here yet.

• Oscar Hur and Kevin Karplus. Methods of translating NMR proton distances into their corresponding heavy atom distances for protein structure prediction with limited experimental data. Protein Engineering, Design and Selection 18(12):597-605, Dec 2005. doi:10.1093/protein/gzi068 Abstract PDF
• Kevin Karplus, Sol Katzman, George Shackleford, Martina Koeva, Jenny Draper, Bret Barnes, Marcia Soriano, and Richard Hughey. SAM-T04: what's new in protein-structure prediction for CASP6. Proteins: Structure, Function, and Bioinformatics, 2005. accepted for CASP6 special issue, in press. Pre-publication copy
• Kevin Karplus, Rachel Karchin, George Shackleford, and Richard Hughey.
  Calibrating E-values for hidden Markov models with reverse-sequence null models.
  Bioinformatics, 2004.
  accepted, final version not to publisher yet.
• T. J. Dolinksy, P. M. J. Burgers, K. Karplus, and N. A. Baker.
  SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome.
  Bioinformatics, 20:2312-2314, April 2004.
• Rachel Karchin, Melissa Cline, and Kevin Karplus.
  Evaluation of local structure alphabets based on residue burial.
  Proteins: Structure, Function, and Genetics, 55(3):508-518, 5 March 2004.
  Online: http://www3.interscience.wiley.com/cgi-bin/abstract/107632554/ABSTRACT
• Kevin Karplus, Rachel Karchin, Jenny Draper, Jonathan Casper, Yael Mandel-Gutfreund, Mark Diekhans, and Richard Hughey.
  Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction.
  Proteins: Structure, Function, and Genetics, 53(Suppl. 6, pages=491-496), 15 October 2003.
• Rachel Karchin, Melissa Cline, Yael Mandel-Gutfreund, and Kevin Karplus.
  Hidden Markov models that use predicted local structure for fold recognition: alphabets of backbone geometry.
  Proteins: Structure, Function, and Genetics, 51(4):504-514, June 2003.
• Kevin Karplus.
  Predicting protein structure using SAM, UCSC's hidden Markov model tools.
  In Igor F. Tsigelny, editor, Protein Structure Prediction: Bioinformatic Approach, IUL Biotechnology Series, pages 297-323. International University Line, La Jolla, California, 2002.
• Melissa Cline, Kevin Karplus, Richard Lathrop, Temple Smith, Robert G. Rogers Jr., and David Haussler.
  Information-theoretic dissection of pairwise contact potentials.
  Proteins: Structure, Function, and Genetics, 49(1):7-14, 1 October 2002.
• Melissa Cline, Richard Hughey, and Kevin Karplus.
  Predicting reliable regions in protein sequence alignments.
  Bioinformatics, 18(2):306-314, February 2002.
• R. Karchin, K. Karplus, and D Haussler.
  Classifying g-protein coupled receptors with support vector machines.
  Bioinformatics, 18(1):147-159, January 2002.
• Julian Gough, Kevin Karplus, Richard Hughey, and Cyrus Chothia.
  Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.
  Journal of Molecular Biology, 313(4):903-919, 2 Nov 2001.
• Richard Hughey and Kevin Karplus.
  Bioinformatics: A new field in engineering education.
  In 31st ASEE/IEEE Frontiers in Education Conference, pages F2B-15-F2B-19, October 2001.
• J.E. Cleaver, K. Karplus, M. Kashani-Sabet, and C. Limoli.
  Nucleotide excision repair, ``a legacy of creativity''.
  Mutation Research/DNA Repair, 485(1):23-36, 25 February 2001.
• Kevin Karplus and Birong Hu.
  Evaluation of protein multiple alignments by SAM-T99 using the BaliBASE multiple alignment test set.
  Bioinformatics, 17:713-720, August 2001.
• Kevin Karplus, Rachel Karchin, Christian Barrett, Spencer Tu, Melissa Cline, Mark Diekhans, Leslie Grate, Jonathan Casper, and Richard Hughey.
  What is the value added by human intervention in protein structure prediction?
  Proteins: Structure, Function, and Genetics, 45(S5):86-91, 2001.
• Chang Zhu, Kevin Karplus, Leslie Grate, and Philip Coffino.
  A homolog of mammalian antizyme is present in fission yeast Schizosaccharomyces pombe but not detected in budding yeast Saccharomyces cerevisiae.
  Bioinformatics, 16(5):478-481, 2000.
• Richard Hughey, Kevin Karplus, and Anders Krogh.
  SAM: Sequence alignment and modeling software system, version 3.
  Technical Report UCSC-CRL-99-11, University of California, Santa Cruz, Computer Engineering, UC Santa Cruz, CA 95064, October 1999.
  Available from http://www.cse.ucsc.edu/research/compbio/sam.html
• Kevin Karplus, Christian Barrett, and Melissa Cline.
  Getting the most out of hidden Markov models.
  In ISMB99 tutorial, Heidelberg, Germany, August 1999.
• Kevin Karplus, Christian Barrett, Melissa Cline, Mark Diekhans, Leslie Grate, and Richard Hughey.
  Predicting protein structure using only sequence information.
  Proteins: Structure, Function, and Genetics, Supplement 3(1):121-125, 1999.
• Daniel Fischer, Christian Barrett, Kevin Bryson, Arne Elofsson, Adam Godzik, David Jones, Kevin Karplus, Lawrence A. Kelley, Robert M. MacCallum, Krzysztof Pawlowski, Burkhard Rost, Leszek Rychlewski, and Michael Sternberg.
  CAFASP-1: Critical assessment of fully automated structure prediction methods.
  Proteins: Structure, Function, and Genetics, Supplement 3(1):209-217, 1999.
• Kevin Karplus, Christian Barrett, and Richard Hughey.
  Hidden Markov models for detecting remote protein homologies.
  Bioinformatics, 14(10):846-856, 1998.
• J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard, and C. Chothia.
  Sequence comparisons using multiple sequences detect twice as many remote homologues as pairwise methods.
  Journal of Molecular Biology, 284(4):1201-1210, 1998.
  http://www.mrc-lmb.cam.ac.uk/genomes/jong/assess_paper/assess_paperNov.html (Link appears to be obsolete.)
• Melissa Cline and Kevin Karplus.
  On alignment shift and its measures.
  Technical Report UCSC-CRL-97-27, University of California, Santa Cruz, Jack Baskin School of Engineering, UC Santa Cruz, CA 95064, February 1998.
• Christian Barrett, Richard Hughey, and Kevin Karplus.
  Scoring hidden Markov models.
  CABIOS, 13(2):191-199, 1997.
• J. A. Grice and R. Hughey and D. Speck.
  Reduced space sequence alignment
  CABIOS, 13(1):45-53, Feb. 1997.
• Kevin Karplus, Kimmen Sjölander, Christian Barrett, Melissa Cline, David Haussler, Richard Hughey, Liisa Holm, and Chris Sander.
  Predicting protein structure using hidden Markov models.
  Proteins: Structure, Function, and Genetics, Suppl. 1:134-139, 1997.
• Kevin Karplus, Kimmen Sjölander, Christian Barrett, Melissa Cline, David Haussler, Richard Hughey, Liisa Holm, and Chris Sander.
  Predicting protein structure using hidden Markov models, the CASP2 contest.
  Technical Report UCSC-CRL-97-13, University of California, Santa Cruz, Computer Science, UC Santa Cruz, CA 95064, November 1997.
• K. Sjölander, K. Karplus, M. P. Brown, R. Hughey, A. Krogh, I. S. Mian, and D. Haussler.
  Dirichlet mixtures: A method for improving detection of weak but significant protein sequence homology.
  Computer Applications in the Biosciences, 12(4):327-345, August 1996.
• Christian Barrett, Richard Hughey, and Kevin Karplus.
  Scoring hidden Markov models.
  In Proceedings, 4th International Conference on Intelligent Systems for Molecular Biology, page poster only, St. Louis, MO, June 1996. AAAI.
• Kevin Karplus, Kimmen Sjölander, Richard Hughey, and Leslie Grate.
  Stochastic modeling techniques: Understanding and using hidden Markov models.
  In Proceedings, 4th International Conference on Intelligent Systems for Molecular Biology, page Tutorial, St. Louis, MO, June 1996.
• Philipp Bucher, Kevin Karplus, Nicolas Moeri, and Kay Hoffman.
  A flexible motif search technique based on generalized profiles.
  Computers and Chemistry, 20(1):3-24, January 1996.
• Kevin Karplus.
  Regularizers for estimating distributions of amino acids from small samples.
  In Proceedings, 3rd International Conference on Intelligent Systems for Molecular Biology, pages 188-196, Cambridge, England, July 1995.
• Kevin Karplus.
  Regularizers for estimating distributions of amino acids from small samples.
  Technical Report UCSC-CRL-95-11, University of California, Santa Cruz, March 1995.
• Kevin Karplus.
  Using Markov models and hidden Markov models to find repetitive extragenic palindromic sequences in Escherichia coli.
  Technical Report UCSC-CRL-94-24, Computer Engineering Department, University of California, Santa Cruz, Santa Cruz, CA 95064, July 1994.

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