Journal Club: Difference between revisions

From MDWiki
Jump to navigationJump to search
Line 9: Line 9:


=== Paper(s) for the <u>next</u> Journal Club ===
=== Paper(s) for the <u>next</u> Journal Club ===
== September 09 ==
# Buchete N.V. ''et al.'' (2005) [[Media:Buchete_JMB2005.pdf|Molecular dynamics simulations of Alzheimer's &beta;-amyloid protofilaments.]] ''J. Mol. Biol.'' '''353''', 804&ndash;821
# Lemkul J.A. &amp; Bevan D.R. (2008) [[Media:Lemkul_ABB2007.pdf|A comparative molecular dynamics analysis of the amyloid &beta;-peptide in a lipid bilayer.]] ''Arch. Biochem. Biophys.'' '''470''', 54&ndash;63
=== Past Journal Clubs ===


=== August 09 ===
=== August 09 ===
Line 14: Line 21:
# Jaynes, ET (1957) [[Media:Jaynes_PhysRev1957-2.pdf|Information theory and statistical mechanics. II.]] ''Phys. Rev.'' '''108'''(2), 171-190
# Jaynes, ET (1957) [[Media:Jaynes_PhysRev1957-2.pdf|Information theory and statistical mechanics. II.]] ''Phys. Rev.'' '''108'''(2), 171-190


=== Past Journal Clubs ===


=== July 09 ===
=== July 09 ===


# U.H.E. Hansmann and Y. Okanoto, (1993) [[Media:Hansmann93.pdf| Prediction of Peptide Conformation by Multicanonical Algorithm: A New Approach to the Multiple-Minima Problem]]. ''J. Comput. Chem.'' '''14''', 1333
# Hansmann U.H.E. ''et al.'' (1993) [[Media:Hansmann93.pdf| Prediction of Peptide Conformation by Multicanonical Algorithm: A New Approach to the Multiple-Minima Problem]]. ''J. Comput. Chem.'' '''14''', 1333
# Ulrich H.E. Hansmann, Yuko Okamoto, Frank Eisenmenger (1996) [[Media:Hansmann96.pdf| Molecular dynamics, Langevin and hybrid Monte Carlo simulations in a multicanonical ensemble]]. ''Chem. Phys. Lett/'' '''259''', 321-330
# Hansmann U.H.E. ''et al.'' (1996) [[Media:Hansmann96.pdf| Molecular dynamics, Langevin and hybrid Monte Carlo simulations in a multicanonical ensemble]]. ''Chem. Phys. Lett/'' '''259''', 321-330
# Ayori Mitsutake and Yuko Okamoto (2009) [[Media:Okamoto09.pdf| From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering]]. ''Phys. Rev. E'' '''79''', 047701
# Mitsutake A. &amp; Okamoto, Y. (2009) [[Media:Okamoto09.pdf| From multidimensional replica-exchange method to multidimensional multicanonical algorithm and simulated tempering]]. ''Phys. Rev. E'' '''79''', 047701




=== June 09 ===
=== June 09 ===


#Joosten and Vriend (2007) [[Media:Joosten_Science2007.pdf| PDB Improvement Starts with Data Deposition.]] ''Science'' '''317''', 195-196
#Joosten &amp; Vriend (2007) [[Media:Joosten_Science2007.pdf| PDB Improvement Starts with Data Deposition.]] ''Science'' '''317''', 195-196
#Joosten et al. (2009)[[Media:Joosten_ActaCrystallogrD2009.pdf‎| Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.]] ''Acta Crystallogr.'' '''D65''', 176-185
#Joosten ''et al.'' (2009)[[Media:Joosten_ActaCrystallogrD2009.pdf‎| Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.]] ''Acta Crystallogr.'' '''D65''', 176-185
#Joosten et al. (2009)[[Media:Joosten_JApplCrystal2009.pdf‎| PDB_REDO: automated re-refinement of X-ray structure models in the PDB.]] ''J. Appl. Cryst.'' '''42''', 376-384
#Joosten ''et al.'' (2009)[[Media:Joosten_JApplCrystal2009.pdf‎| PDB_REDO: automated re-refinement of X-ray structure models in the PDB.]] ''J. Appl. Cryst.'' '''42''', 376-384


==== May 09 ====
==== May 09 ====


# Omabegho et al. (2009) [[Media:JournalClub_Omabegho2009.pdf|A bipedal DNA Brownian motor with coordinated legs.]] ''Science'' '''324''', 67-71
# Omabegho ''et al.'' (2009) [[Media:JournalClub_Omabegho2009.pdf|A bipedal DNA Brownian motor with coordinated legs.]] ''Science'' '''324''', 67-71


==== March 09 ====
==== March 09 ====


# Chang et al. (2001) [[Media:MsbA_Chang01.pdf|Structure of MsbA from E. coli: A Homolog of the Multidrug Resistance ATP Binding Cassette (ABC) Transporters.]] ''Science'' '''293''', 1793-1800
# Chang ''et al.'' (2001) [[Media:MsbA_Chang01.pdf|Structure of MsbA from E. coli: A Homolog of the Multidrug Resistance ATP Binding Cassette (ABC) Transporters.]] ''Science'' '''293''', 1793-1800
# Miller (2006) [[Media:MsbA_Miller06.pdf|A Scientist’s Nightmare: Software Problem Leads to Five Retractions.]] ''Science'' '''314''', 1856-1857
# Miller (2006) [[Media:MsbA_Miller06.pdf|A Scientist’s Nightmare: Software Problem Leads to Five Retractions.]] ''Science'' '''314''', 1856-1857
# Petsko (2007) [[Media:MsbA_Petsko07.pdf|And the second shall be first.]] ''Genome Biol.'' '''8''',103
# Petsko (2007) [[Media:MsbA_Petsko07.pdf|And the second shall be first.]] ''Genome Biol.'' '''8''',103
# Jeffrey (2009) [[Media:MsbA_Jeffrey09.pdf|Analysis of errors in the structure determination of MsbA.]] ''Acta Crystallogr.'' '''D65''', 193–199
# Jeffrey (2009) [[Media:MsbA_Jeffrey09.pdf|Analysis of errors in the structure determination of MsbA.]] ''Acta Crystallogr.'' '''D65''', 193–199

Revision as of 05:48, 8 September 2009

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 next Journal Club

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


Past Journal Clubs

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
Retrieved from "http://compbio.biosci.uq.edu.au/mediawiki/index.php?title=Journal_Club&oldid=15355"