CTBP Journal Club Schedule: Academic Year 2005

Main Journal Club Page

06/06/05 - Cameron Mura (McCammon lab)

Article:  "Automatic classification of protein structure by using Gauss integrals", P. Rogen and B. Fain, PNAS, 100, 119-123 (2003).

05/23/05 -  Daniel Hill (Kleinfeld lab)

Article:  "Attractor dynamics in the hippocampal representation of the local environment", T.J. Wills, F. Cacucci, N. Burgess, and J. O'Keefe, Science, 308, 873-6 (2005).

05/16/05 - Robert White (Hwa and McCammon labs)

Article:  "Comparative metagenomics of microbial communities", S.G. Tringe, C. von Mering, A. Kobayashi, A.A. Salamov, K. Chen, H.W. Chang, M. Podar, J.M. Short, E.J. Mathur, J.C. Detter, P. Bork, P. Hugenholtz, and E.M. Rabin, Science, 308, 554-557 (2005).

05/09/05 - Scott Wylie (Levine lab)

Article: "Genome-wide non-mendelian inheritance of extra-genomic information in Arabidopsis", S. J. Lolle, J. L. Victor, J. M. Young, and R. E. Pruitt, Nature, 434, 505-509 (2005).

04/25/05 - Shachi Gosavi (Onuchic lab)

Article: "Force-Clamp Spectroscopy Monitors the Folding Trajectory of a Single Protein", J.M. Fernandez and H. Li, Science, 303: 1674-1678 (2004).

04/18/05 - Shaoying Lu (Holst and McCulloch labs)

Article:  "A simplified local control model of calcium-induced calcium release in cardiac ventricular myocytes", R. Hinch, J.L. Greenstein, A.J. Tanskanen, L. Xu, and R.L. Winslow, Biophys. J., 878, 37223-3726 (2004).

04/04/05 - Jessica Swanson (McCammon lab)

Article:  "Hydrophobic Collapse in Multidomain Protein Folding", R Zhou, et al., Science, 305, 1605-1609 (2004).

03/28/05 - Sichun Yang (Levine and Onuchic labs)

Article:  "A neuronal isoform of the aplysia CPEB has prion-like properties", K. Si, S. Lindquist, and E.R. Kandel, Cell, 115, 879-91 (2003).

03/07/05 - Tongye Shen (Wolynes lab)

Article:  "Nonlinear competition between asters and stripes in filament-motor-systems", F. Ziebert and W. Zimmermann, Condensed Matter, abstract cond-mat/00502236 (2005).

02/28/05 - Peter McHale (Levine Lab)

Articles:  "Dpp gradient formation by dynamin-dependent endocytosis: receptor trafficking and the diffusion model", K. Kruse, P Pantazis, T Bollenbach, F Julicher and M Gonzalez-Gaitan, Development 131, 4843 (2004)

"Robust Formation of Morphogen Gradients," T Bollenbach, K Kruse, P Pantazis, M Gonzalez-Gaitan, F Julicher, PRL 94, 018103 (2005)

02/14/05 - Joachim Dzubiella (McCammon lab)

Article:  "'Detection of molecular interactions at membrane surfaces through colloid phase transitions," M. M. Baksh, M. Jaros, and J.T. Groves, Nature, 427, 139 (2004).

02/07/05 - William McLaughlin (Wang lab)

Article:  "Molecular dynamics, free energy, and SPR analyses of the interactions between the SH2 domain of Grb2 and ErbB phosphotyrosyl peptides," A. Suenaga, M. Hatakeyama, M. Ichikawa, X. Yu, N. Futatsugi, T. Narumi, K. Fukui, T. Terada, M. Taiji, M. Shirouzu, S. Yokoyama, and A. Konagaya, Biochemistry 42(18), 5195-200 (2003).

01/31/05 - Cheol-Min Ghim (Hwa lab)

Article:  "Evolutionary Dynamics on Graphs", E. Liberman, C. Hauert, and M. A. Nowak, Nature, 433, 312 (2005). 

01/24/05 - Jennifer Fenwick (Holst lab)

Article:  "A Morphing Algorithm for Generating Near Optimal Grids: Appications in Computational Medicine", S.G. Parker, D.M. Weinsten, and C.R. Johnson, University of Utah Technical Report, UUCS-94-014, 1994.

01/10/05 - Olgun Guvench (Brooks lab)

Article:"Folding Trp-Cage to NMR Resolution Native Structure Using a Coarse-Grained Protein Model", F. Ding, S. V. Buldyrev, andN. V. Dokholyan,  Biophysical Journal, 88:147-155 (2005).

12/06/04 - Qizhi Cui (Case lab)

Article:  "A structural model for the assembly of the 30S subunit of the ribosome,"  S.M. Stagg, J.A. Mears, and S.C. Harvey,  Journal of Molecular Biology, 328, 49-61 (2003).

11/29/04 - David Minh (McCammon lab)

Article:  "Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides," H.D. Nguyen and C. K. Hall, PNAS, Volume 101, No. 46, 16180-16185 (2004).

11/08/04 - Ben-Zhuo Lu (McCammon lab)

Articles:  "Robust Biased Brownian Dynamics for Rate Constant Calculation", G. Zou and R.D. Skeel, Biophysical Journal, Volume 85, 2147-2157 (2003). and "Biased Brownian Dynamics for Rate Constant Calculation", G. Zou, R.D. Skeel and S. Subramaniam, Biophysical Journal, Volume 79, 638-645 (2000).

11/01/04 - Ian Thorpe (Brooks lab)

Article: "An assessment of mean force calculations with implicit solvent models", C.M. Stultz, J. Phys. Chem. B, 108, 16525-16532 (2004).

10/25/04 - Diego Ferreiro (Wolynes lab)

Article:  "Allosteric switching by mutually exclusive folding of protein domains", T.L. Radley, A.I. Markowska, B.T. Bettinger, J.H. Ha, and S.N. Loh, J. Mol. Biol., 332(3), 529-36 (2004).  

10/18/04 - John Mongan (McCammon and Case labs)

Article:  "Constant-pH molecular dynamics using continuous titration coordinates", M.S. Lee, F.R. Salsbury Jr., and C.L. Brooks III, Proteins, 56(4), 738-752 (2004).  

10/11/04 - Wonpil Im (Brooks lab)

 Articles:   "Designing transmembrane alpha-helix that insert spontaneously",  W.C. Wimley and S. H. White, Biochemisty, 39:4432–4442 (2000).   and  "Interfacial folding and membrane insertion of a designed helical peptide", A.S. Ladokhin and S.H. White, Biochemisty, 43:5782–5791 (2004).

10/04/04 - Rolf Olson (Loomis lab)

Article:  "The Mathematical Structure of Reversible Matrices and Its Physical Interpretation", submitted.

09/27/04 - Rex Kerr (Sejnowski Lab)

Article:  "Signaling in Small Subcellular Volumes I: Stocastic and Diffusion Effects of Individual Pathways",  U. Bhalla, Biophysical Journal, 87:733-744 (2004).