Journal Club

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Contents

Schedule

See the Group meeting schedule.

Megan is in charge of the organization of the Journal Club. In no way she is the one to find all the papers for every Journal Club!

Journal Club Papers

Paper(s) for the May 2010 Journal Club

  1. Vassiliev, S, Comte, P, Mahboob, A & Bruce, D (2010) Tracking the flow of water through photosystem II using molecular dynamics and streamline tracing. Biochemistry 9, 1873–1881
  2. Teixeira VH, Baptista AM & Soares CM (2006) Pathways of H2 toward the active site of [NiFe]-hydrogenase. Biophys. J. 91, 2035–2045
  3. Ulitsky, A & Elber, R (1994) Application of the locally enhanced sampling (LES) and a mean field with a binary collision correction (cLES) to the simulation of Ar diffusion and NO recombination in myoglobin. J. Phys. Chem 98, 1034–1043
  4. Ruscio, JZ, Kumar, D, Shukla, M, Prisant, MG, Murali, TM & Onufriev AV (2008) Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin. Proc. Natl. Acad. Sci. U. S. A. 105, 9204–9209


Past Journal Clubs

April 10

  1. Topiol, S et al. (2009) X-ray structure breakthroughs in the GPCR transmembrane region. Biochem Pharmacol. 78, 11-20.

February 10

  1. Hammes-Schiffer, S (2009) Theory of proton-coupled electron transfer in energy conversion processes. Acc. Chem. Res. 42, 1881-1889

November 09

  1. Noble, W.S. (2009) A quick guide to organizing computational biology projects. PLOS Comput. Biol. 5, e1000424

October 09

  1. Chang, G. et al. (1998) Structure of the MscL Homolog from Mycobacterium tuberculosis: A Gated Mechanosensitive Ion Channel. Science 282, 2220–2226
  2. Liu, Z. et al.(2009) Structure of a tetrameric MscL in an expanded intermediate state. Nature 461, 120–126
  3. Vasquez, V. & Perozo, E. (2009) A channel with a twist Nature 461, 47–49

September 09

  1. Buchete N.V. et al. (2005) Molecular dynamics simulations of Alzheimer's β-amyloid protofilaments. J. Mol. Biol. 353, 804–821
  2. Lemkul J.A. & Bevan D.R. (2008) A comparative molecular dynamics analysis of the amyloid β-peptide in a lipid bilayer. Arch. Biochem. Biophys. 470, 54–63

August 09

  1. Jaynes, ET (1957) Information theory and statistical mechanics. Phys. Rev. 106(4), 620-630
  2. Jaynes, ET (1957) Information theory and statistical mechanics. II. Phys. Rev. 108(2), 171-190

July 09

  1. Hansmann U.H.E. et al. (1993) Prediction of Peptide Conformation by Multicanonical Algorithm: A New Approach to the Multiple-Minima Problem. J. Comput. Chem. 14, 1333
  2. Hansmann U.H.E. et al. (1996) Molecular dynamics, Langevin and hybrid Monte Carlo simulations in a multicanonical ensemble. Chem. Phys. Lett/ 259, 321-330
  3. Mitsutake A. & Okamoto, Y. (2009) From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering. Phys. Rev. E 79, 047701

June 09

  1. Joosten & Vriend (2007) PDB Improvement Starts with Data Deposition. Science 317, 195-196
  2. Joosten et al. (2009) Re-refinement from deposited X-ray data can deliver improved models for most PDB entries. Acta Crystallogr. D65, 176-185
  3. Joosten et al. (2009) PDB_REDO: automated re-refinement of X-ray structure models in the PDB. J. Appl. Cryst. 42, 376-384

May 09

  1. Omabegho et al. (2009) A bipedal DNA Brownian motor with coordinated legs. Science 324, 67-71

March 09

  1. Chang et al. (2001) Structure of MsbA from E. coli: A Homolog of the Multidrug Resistance ATP Binding Cassette (ABC) Transporters. Science 293, 1793-1800
  2. Miller (2006) A Scientist’s Nightmare: Software Problem Leads to Five Retractions. Science 314, 1856-1857
  3. Petsko (2007) And the second shall be first. Genome Biol. 8,103
  4. Jeffrey (2009) Analysis of errors in the structure determination of MsbA. Acta Crystallogr. D65, 193–199
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