Theoretical Seminars and Journal Club: Difference between revisions

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=== Schedule ===
== Schedule ==


date | main presenter | topic
date | main presenter | topic
Line 6: Line 6:
See the [[meeting schedule|Group meeting schedule]].
See the [[meeting schedule|Group meeting schedule]].


== Journal Club Papers ==


----
=== Papers for the <u>next</u> Journal Club ===


=== Suggested Topics ===
''More to come soon...''
 
=== Past Journal Clubs ===
 
==== 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
# 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
# Jeffrey (2009) [[Media:MsbA_Jeffrey09.pdf|Analysis of errors in the structure determination of MsbA]] ''Acta Crystallogr.'' '''D65''', 193–199
 
== Suggested Topics ==


name of topic | suggestion by
name of topic | suggestion by
Line 27: Line 39:
6. Error in Crystal Structures and its implications. Can MD be used for X-ray structure refinement?
6. Error in Crystal Structures and its implications. Can MD be used for X-ray structure refinement?


----
== The paper pool ==
 
=== The paper pool ===


Author | Title | Topic area | DOI URL |
Author | Title | Topic area | DOI URL |


# Beutler TC, Mark A.E., van Schaik R.C., Gerber P.R. and van Gunsteren W.F. (1994) Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. ''Chem. Phys. Lett.'' '''222''' (6), 529-539. [http://dx.doi.org/10.1016/0009-2614(94)00397-1 [link]]
# Alber F., F&ouml;rster F., Korkin D., Topf M. and Sali A. (2008) [[Media:Alber_AnnuRevBiochem08.pdf|Integrating diverse data for structure determination of macromolecular assemblies.]] ''Annu. Rev. Biochem.'' '''77'', 443-477.
# Tropp J. (1980) [[Media:Tropp_JChemPhys80.pdf|Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances.]] ''J. Chem. Phys.'' '''72''' (11), 6035-6043.
# Daura X, Antes I, van Gunsteren WF, Thiel W and Mark AE. (1999) The effect of motional averaging on the calculation of NMR-derived structural properties. ''Proteins'' '''36''' (4), 542-55.
# Hirsch M. and Habeck M. (2008) [[media:Mixture_models.pdf | Mixture models for protein structure ensembles]]. ''Bioinformatics'' '''24''' (19), 2184–2192.
# Rieping W., Habeck M. and Nilges M. (2005) [[media:Modeling_errors_in_NOE.pdf | Modeling Errors in NOE Data with a Log-normal Distribution Improves the Quality of NMR Structures]]. ''J. Am. Chem. Soc.'', '''127''', 16026-16027
# Davis A.M., St-Gallay S.A. and Kleywegt G.J. (2008) [[Media:Davis_DrugDiscovToday08.pdf|Limitations and lessons in the use of X-ray structural information in drug design.]] ''Drug Discov. Today'' '''13''' (19/20), 831-841.
# Davis A.M., Teague S.J. and Kleywegt G.J. (2003) [[Media:Davis_AngewChemIntEd03.pdf|Application and limitations of X-ray crystallographic data in structure-based ligand and drug design.]] ''Angew. Chem. Int. Ed.'' '''42''', 2718-2736.
# Sokal A.D. (1996) [[media:Sokal-transgressing-boundaries.pdf | Transgressing the Boundaries: Towards a Transformative Hermeneutics of Quantum Gravity]] ''Social Text'' '''46/47''', 217-252.
# Ma, J. (2005) [[media:Usefulness_and_Limitations_of_Normal_Mode_Analysis_in_Modeling_Dynamics_of_Biomolecular_Complexes.pdf|Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes.]] ''Structure'' '''13''' 373-380.
# Kitao A. and Go N. (1999) [[media:Investigating_protein_dynamics_in_collective_coordinate_space.pdf|Investigating protein dynamics in collective coordinate space.]] ''Curr. Opin. Struct. Biol.''  '''9''' (2), 164-169.
# Hess B. (2002) [[Media:Convergence_of_sampling_in_protein_simulations.pdf|Convergence of sampling in protein simulations.]] ''Phys. Rev. E'' '''65''', 031910.
# Aloy P. and Russell R.B. (2006) [[Media:Aloy_NatRevMolCellBiol2006.pdf|Structural systems biology: modelling protein interactions.]] ''Nat. Rev. Mol. Cell. Biol.'' '''7''' (3), 188-197.
# Zaccai G. (2000) [[Media:Zaccai_Science2000.pdf|How soft is a protein? A protein dynamics force constant measured by neutron scattering.]] ''Science'' '''288''' (5471), 1604-1607.


== The Theoretical Seminars Lectures ==


1.  BEUTLER TC, MARK AE, VANSCHAIK RC, et al. AVOIDING SINGULARITIES AND NUMERICAL INSTABILITIES IN FREE-ENERGY CALCULATIONS BASED ON MOLECULAR SIMULATIONS.
=== Clustering methods (Itamar Kass, 30.10.08)===
CHEMICAL PHYSICS LETTERS, 1994, 222 (6) : 529-539.
*PDF file of the talk [[Media:Clustering_methods.pdf|here]]
http://dx.doi.org/10.1016/0009-2614(94)00397-1
*Complementary reading:
 
*#[[media:Algorithms_for_Clustering_Molecular_Dynamics_Configurations_.pdf| Torda, AE and van Gunsrteren, WF (1994) Algorithms for clustering molecular dynamics configurations. ''J. Comput. Chem.'' '''15''' (12), 1331-1340]]
2. Frank Alber, ­ Friedrich Förster, ­ Dmitry Korkin, Maya Topf and ­ Andrej Sali Integrating Diverse Data for Structure Determination of Macromolecular Assemblies
*#[[media:Clustering_molecular_dynamics_trajectories-_I._Characterizing_the_performance_of_different_clustering_algorithms.pdf‎| Shao, J ''et al'' (2007) Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. ''J. Chem. Theory Comput.'' '''3''', 2312-2334]]
Annual Review of Biochemistry
*#[[media:Peptide_Folding-_When_Simulation_Meets_Experiment.pdf‎| Daura, X ''et al'' (1999) Peptide folding: when simulation meets experiment. ''Angew. Chem. Int. Ed.'' '''38'' (1/2), 236-240]]
http://dx.doi.org/10.1146/annurev.biochem.77.060407.135530
 
3. Tropp J. (1980) Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances. ''J. Chem. Phys.'' '''72''', 6035
http://link.aip.org/link/?JCPSA6/72/6035/1
 
4. Daura X, Antes I, van Gunsteren WF, Thiel W, Mark AE. (1999) The effect of motional averaging on the calculation of NMR-derived structural properties. ''Proteins'' '''36'''(4), 542-55
http://dx.doi.org/10.1002/(SICI)1097-0134(19990901)36:4<542::AID-PROT17>3.0.CO;2-M
 
5. Michael Hirsch and Michael Habeck (2008) [[media:Mixture_models.pdf | Mixture models for protein structure ensembles]].
''Bioinformatics'' Vol. 24 no. 19 2008, pages 2184–2192.
 
6. Wolfgang Rieping, Michael Habeck and Michael Nilges (2005) [[media:Modeling_errors_in_NOE.pdf | Modeling Errors in NOE Data with a Log-normal Distribution Improves the Quality of NMR Structures]].
''JACS'', '''127''', 16026-16027
 
7. Davis A, St-Gallay SA, Kleywegt GJ. "Limitations and lessons in the use of X-ray structural information in drug design". Drug Discovery Today, 2008, 19/20, 831.
http://dx.doi.org/10.1016/j.drudis.2008.06.006
 
8. Davis AM, Teague SJ, Kleywegt GJ. "Application and Limitations of X-ray crystallographic data in structure-based ligand and drug design". Angew. Chem. Intl. Ed., 2003, 42, 2718.
http://www3.interscience.wiley.com/cgi-bin/fulltext/104539506/PDFSTART
DOI: 10.1002/anie.200200539
 
9. Alan D. Sokal (1996) [[media:Sokal-transgressing-boundaries.pdf | Transgressing the Boundaries: Towards a Transformative Hermeneutics of Quantum Gravity]] ''Social Text'' '''46/47''', 217-252.
 
----


=== The paper pool ===
=== Prediction of secondary structures (David Poger, 16.04.09) ===


30 October 2008,Itamar Kass, Clustering methods [[Media:Clustering_methods.pdf]].
''More to come soon...''

Latest revision as of 23:50, 23 March 2009

Schedule

date | main presenter | topic


See the Group meeting schedule.

Journal Club Papers

Papers for the next Journal Club

More to come soon...

Past Journal Clubs

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

Suggested Topics

name of topic | suggestion by


1. Soft Core non-bonded interactions - Alpesh

2. Structural Determination - Mitchell

3. How to define Clusters and what can we learn from it on proteins properties? - Itamar

4. Gromacs 4: What's new - What's broken?

Breaking the 2fs time step barrier and clever parallelisation.

5. GROMOS2017 - Coming soon(ish)! - New developments

6. Error in Crystal Structures and its implications. Can MD be used for X-ray structure refinement?

The paper pool

Author | Title | Topic area | DOI URL |

  1. Beutler TC, Mark A.E., van Schaik R.C., Gerber P.R. and van Gunsteren W.F. (1994) Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations. Chem. Phys. Lett. 222 (6), 529-539. [link]
  2. Alber F., Förster F., Korkin D., Topf M. and Sali A. (2008) Integrating diverse data for structure determination of macromolecular assemblies. Annu. Rev. Biochem. '77, 443-477.
  3. Tropp J. (1980) Dipolar relaxation and nuclear Overhauser effects in nonrigid molecules: The effect of fluctuating internuclear distances. J. Chem. Phys. 72 (11), 6035-6043.
  4. Daura X, Antes I, van Gunsteren WF, Thiel W and Mark AE. (1999) The effect of motional averaging on the calculation of NMR-derived structural properties. Proteins 36 (4), 542-55.
  5. Hirsch M. and Habeck M. (2008) Mixture models for protein structure ensembles. Bioinformatics 24 (19), 2184–2192.
  6. Rieping W., Habeck M. and Nilges M. (2005) Modeling Errors in NOE Data with a Log-normal Distribution Improves the Quality of NMR Structures. J. Am. Chem. Soc., 127, 16026-16027
  7. Davis A.M., St-Gallay S.A. and Kleywegt G.J. (2008) Limitations and lessons in the use of X-ray structural information in drug design. Drug Discov. Today 13 (19/20), 831-841.
  8. Davis A.M., Teague S.J. and Kleywegt G.J. (2003) Application and limitations of X-ray crystallographic data in structure-based ligand and drug design. Angew. Chem. Int. Ed. 42, 2718-2736.
  9. Sokal A.D. (1996) Transgressing the Boundaries: Towards a Transformative Hermeneutics of Quantum Gravity Social Text 46/47, 217-252.
  10. Ma, J. (2005) Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13 373-380.
  11. Kitao A. and Go N. (1999) Investigating protein dynamics in collective coordinate space. Curr. Opin. Struct. Biol. 9 (2), 164-169.
  12. Hess B. (2002) Convergence of sampling in protein simulations. Phys. Rev. E 65, 031910.
  13. Aloy P. and Russell R.B. (2006) Structural systems biology: modelling protein interactions. Nat. Rev. Mol. Cell. Biol. 7 (3), 188-197.
  14. Zaccai G. (2000) How soft is a protein? A protein dynamics force constant measured by neutron scattering. Science 288 (5471), 1604-1607.

The Theoretical Seminars Lectures

Clustering methods (Itamar Kass, 30.10.08)

Prediction of secondary structures (David Poger, 16.04.09)

More to come soon...

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