662 References
[679] D. Kosztin, T. C. Bishop, and K. Schulten. Binding of the estrogen receptor to
DNA: The role of waters. Biophys. J., 73:557–570, 1997.
[680] R. Z. Kramer, J. Bella, B. Brodsky, and H. M. Berman. The crystal and molecular
structure of a collagen-like peptide with a biologically relevant sequence. J. Mol.
Biol., 311:131–147, 2001.
[681] M. Kr¨oger, A. Alba-Perez, M. Laso, and H. C.
¨
Ottinger. Variance reduced
Brownian simulation of a bead-spring chain under steady shear flow considering
hydrodynamic interaction effects. J. Chem. Phys., 113:4767–4773, 2000.
[682] M. Kruithof, F.-T. Chen, A. Routh, C. Logie, D. Rhodes, and J. van Noort. Single-
molecule force microscopy reveals a highly compliant helical folding for the
30-nm chromatin fiber. Nat. Struc. Mol. Biol., 16:534–540, 2009.
[683] A. Kryshtafovych, K. Fidelis, and J. Moult. Progress from CASP6 to CASP7.
Proteins: Struc. Func. Gen., 69 (Suppl. 8):194–207, 2007.
[684] R. Kubo. The fluctuation-dissipation theorem. Rep. Prog. Phys., 29:255–284,
1966.
[685] W. K ¨uhlbrandt and K. A. Williams. Analysis of macromolecular structure and
dynamics by electron cryo-microscopy. Curr. Opin. Chem. Biol., 3:537–543, 1999.
[686] P. Kumar, H.-S. Ban, S.-S. Kim, H. Wu, T. Pearson, D. L. Greiner, A. Laouar,
J. Yao, V. Haridas, K. Habiro, Y.-G. Yang, J.-H. Jeong, K.-Y. Lee, Y.-H. Kim,
S. W. Kim, M. Peipp, G. H. Fey, N. Manjunath, L. D. Shultz, and S.-K. Lee. T
cell-specific siRNA delivery suppresses HIV-1 infection in humanized mice. Cell,
134:577–586, 2008.
[687] P. D. Kwong, R. Wyatt, J. Robinson, R. W. Sweet, J. Sodroski, and W. A.
Hendrickson. Structure of an HIV gp 120 envelope glycoprotein in complex with
the CD4 receptor and a neutralizing human antibody. Nature, 393:648–659, 1998.
[688] L. J. LaBerge and J. C. Tully. A rigorous procedure for combining molecular
dynamics and Monte Carlo simulation algorithms. Chem. Phys., 260:183–191,
2000.
[689] A. Laederach. Informatics challenges in structured RNAs. Brief. Bioinf.,
8:294–303, 2007.
[690] C. Laing, S. Jung, A. Iqbal, and T. Schlick. Tertiary motifs revealed in analyses of
higher-order RNA junctions. J. Mol. Biol., 393:67–82, 2009.
[691] C. Laing and T. Schlick. Analysis of four-way junctions in RNA structures. J. Mol.
Biol., 390:547–559, 2009.
[692] M. L. Lamb, K. W. Burdick, S. Toba, M. M. Young, A. G. Skillman, X. Zou,
J. R. Arnold, and I. D. Kuntz. Design, docking, and evaluation of multiple libraries
against multiple targets. Proteins: Struc. Func. Gen., 42:296–318, 2001.
[693] C. G. Lambert, T. A. Darden, and J. A. Board, Jr. A multipole-based algorithm for
efficient calculation of forces and potentials in macroscopic periodic assemblies of
particles. J. Comput. Phys., 126:274–285, 1996.
[694] L. D. Landau and E. M. Lifshitz. Course of Theoretical Physics, volume 5.
Pergamon Press, Oxford, third edition, 1980.
[695] E. Lander. The new genomics: Global views of biology. Science, 274:536–539,
1996.