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Team:EPF-Lausanne/Information & references
From 2009.igem.org
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# Atsushi Yamamoto, Tatsuya Iwata, Satoru Tokutomi and Hideki Kandori, '''Role of Phe1010 in Light-Induced Structural Changes of the neo1-LOV2 Domain of Adiantum''' Biochemistry, 2008, 47 (3), pp 922–928 ([http://pubs.acs.org/doi/full/10.1021/bi701851v Article]) | # Atsushi Yamamoto, Tatsuya Iwata, Satoru Tokutomi and Hideki Kandori, '''Role of Phe1010 in Light-Induced Structural Changes of the neo1-LOV2 Domain of Adiantum''' Biochemistry, 2008, 47 (3), pp 922–928 ([http://pubs.acs.org/doi/full/10.1021/bi701851v Article]) | ||
# Brian D Zoltowski, Brian Vaccaro & Brian R Crane, '''Mechanism-based tuning of a LOV domain photoreceptor''' Published online: 30 August 2009 | doi:10.1038/nchembio.210 ([http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.210.html Article]) | # Brian D Zoltowski, Brian Vaccaro & Brian R Crane, '''Mechanism-based tuning of a LOV domain photoreceptor''' Published online: 30 August 2009 | doi:10.1038/nchembio.210 ([http://www.nature.com/nchembio/journal/vaop/ncurrent/full/nchembio.210.html Article]) | ||
| - | # Michael P. Allen, '''Introduction to Molecular Dynamics Simulation''' published in Computational Soft Matter: From Synthetic Polymers to Proteins, Lecture Notes, Norbert Attig, Kurt Binder, Helmut Grubmüller, Kurt Kremer(Eds.), John von Neumann Institute for Computing, Jülich, NIC Series, Vol. 23, ISBN3-00-012641-4, pp. 1-28, 2004. | + | # Michael P. Allen, '''Introduction to Molecular Dynamics Simulation''' published in Computational Soft Matter: From Synthetic Polymers to Proteins, Lecture Notes, Norbert Attig, Kurt Binder, Helmut Grubmüller, Kurt Kremer(Eds.), John von Neumann Institute for Computing, Jülich, NIC Series, Vol. 23, ISBN3-00-012641-4, pp. 1-28, 2004. ([[Media:Introduction_to_molecular_Dynamics_Simulation.pdf |Article]]) |
===VMD informations=== | ===VMD informations=== | ||
Revision as of 16:26, 19 October 2009
LOV2 & LOVTAP references
- Strickland et al. Light-activated DNA binding in a designed allosteric protein. Proceedings of the National Academy of Sciences (2008) vol. 105 (31) pp. 10709 (Article)
- Freddolino, P.L., Dittrich M., Schulten K., Dynamic Switching Mechanisms in LOV1 and LOV2 Domains of Plant Phototropins. Biophysical Journal, 91, 3630-3639, 2006 (Article)
- Atsushi Yamamoto, Tatsuya Iwata, Satoru Tokutomi and Hideki Kandori, Role of Phe1010 in Light-Induced Structural Changes of the neo1-LOV2 Domain of Adiantum Biochemistry, 2008, 47 (3), pp 922–928 (Article)
- Brian D Zoltowski, Brian Vaccaro & Brian R Crane, Mechanism-based tuning of a LOV domain photoreceptor Published online: 30 August 2009 | doi:10.1038/nchembio.210 (Article)
- Michael P. Allen, Introduction to Molecular Dynamics Simulation published in Computational Soft Matter: From Synthetic Polymers to Proteins, Lecture Notes, Norbert Attig, Kurt Binder, Helmut Grubmüller, Kurt Kremer(Eds.), John von Neumann Institute for Computing, Jülich, NIC Series, Vol. 23, ISBN3-00-012641-4, pp. 1-28, 2004. (Article)
VMD informations
VMD is used to visualize molecules. It is quite user friendly.
- A tutorial for VMD can be found here.
NAMD informations
NAMD performs minimization and equilibration.
- A tutorial is on the same page as for VMD, here.
- NAMD 2.7b1 User's Guide
- Summary of parameters setting
Run a simulation
A simulation is composed of different steps. Here are a few links that deal with heating and stabilization.
- Building Gramicidin A: Equilibration: protocol uses a single .conf file, heating process is too fast.
- NAMD notes from Robinson Lab: a really nice heating process, but involves different .conf files, which is really painful.
