UCSC BME 220 Spring 2007

List of papers for journal club presentations

(Last Update: 13:01 PDT, 21 May 2007 )
  1. Jeffrey PD, Russo AA, Polyak K, Gibbs E, Hurwitz J, Massague J, Pavletich NP.
    Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex.
    Nature 376, 313-320, 1995.
    doi:10.1038/376313a0

  2. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M.
    Crystal structure of rhodopsin: A G protein-coupled receptor.
    Science 289, 739-745, 2005.
    doi:10.1126/science.289.5480.739

  3. Horita DA, Baldisseri DM, Zhang W, Altieri AS, Smithgall TE, Gmeiner WH, Byrd RA.
    Solution structure of the human Hck SH3 domain and identification of its ligand binding site.
    J Mol Biol 278, 253-265, 1998.
    doi:10.1006/jmbi.1998.1690

  4. Denning DP, Patel SS, Uversky V, Fink AL, Rexach M.
    Disorder in the nuclear pore complex: the FG repeat regions of nucleoporins are natively unfolded.
    Proc Natl Acad Sci U S A 100, 2450-5, 2003.
    doi:10.1073/pnas.0437902100

  5. Bower MJ, Cohen FE, Dunbrack RL Jr.
    Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.
    J Mol Biol 267, 1268-1282, 1997.
    doi:10.1006/jmbi.1997.0926

  6. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D.
    Gapped BLAST and PSI-BLAST: A new generation of protein database search programs.
    Nucleic Acids Res 25, 3389-3402, 1997.

  7. Karlin S, Altschul SF.
    Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes.
    Proc Natl Acad Sci U S A 87, 2264-2268, 1990.

  8. Simons KT, Kooperberg C, Huang E, Baker D.
    Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.
    J Mol Biol 268, 209-225, 1997.
    A HREF="http://dx.doi.org/10.1006/jmbi.1997.0959">doi:10.1006/jmbi.1997.0959

  9. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D.
    Design of a novel globular protein fold with atomic-level accuracy.
    Science 302, 1364-1368, 2003.
    doi:10.1126/science.1089427

  10. Cline MS, Karplus K, Lathrop RH, Smith TF, Rogers Jr. RG, Haussler D.
    Information-theoretic dissection of pairwise contact potentials.
    Proteins: Structure, Function, and Genetics 49, 7-14, 2002.
    doi:10.1002/prot.10198

  11. Henikoff S, Henikoff JG.
    Amino acid substitution matrices from protein blocks.
    Proc Natl Acad Sci U S A 89, 10915-10919, 1992.

  12. Henikoff S, Henikoff JG.
    Position-based sequence weights.
    J Mol Biol 243, 574-578, 1994.
    doi:10.1016/0022-2836(94)90032-9

  13. Altschul SF.
    Amino acid substitution matrices from an information theoretic perspective.
    J Mol Biol 219, 555-565, 1991.
    doi:10.1016/0022-2836(91)90193-A (only abstract available from JMB: here is a badly scanned PDF copy

  14. Sippl M.
    Knowledge-based potentials for proteins.
    Curr Opin Struct Biol 5, 229-235, 1995.

  15. Stefan J. Suhrer , Markus Wiederstein and Manfred J. Sippl.
    QSCOP---SCOP quantified by structural relationships.
    Bioinformatics> 23(4):513-514, 2007.
    doi:10.1093/bioinformatics/btl594

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Kevin Karplus
Biomolecular Engineering
University of California, Santa Cruz
Santa Cruz, CA 95064
USA
karplus@soe.ucsc.edu
1-831-459-4250