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Team:EPF-Lausanne/Information & references
From 2009.igem.org
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# 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 [[Media:Light-activated.pdf | Article]] | # 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 [[Media:Light-activated.pdf | 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 ([http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=PMC1630464 Pubmed]) | # Freddolino, P.L., Dittrich M., Schulten K., '''Dynamic Switching Mechanisms in LOV1 and LOV2 Domains of Plant Phototropins'''. Biophysical Journal, 91, 3630-3639, 2006 ([http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=PMC1630464 Pubmed]) | ||
| - | # 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 | + | # 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]) |
===VMD informations=== | ===VMD informations=== | ||
Revision as of 14:53, 18 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 ([http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=PMC1630464 Pubmed])
- 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])
VMD informations
VMD is used to visualize molecules. It is quite user friendly.
- A tutorial for VMD can be found [http://www.ks.uiuc.edu/Training/Tutorials/ here].
NAMD informations
NAMD performs minimization and equilibration.
- A tutorial is on the same page as for VMD, [http://www.ks.uiuc.edu/Training/Tutorials/ here].
- [http://www.ks.uiuc.edu/Research/namd/2.7b1/ug/ 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.
- [http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/ Building Gramicidin A: Equilibration]: protocol uses a single .conf file, heating process is too fast.
- [http://www.biochemistry.uab.edu/robinson/documents/howto/modeling/NAMD_notes.htm NAMD notes from Robinson Lab]: a really nice heating process, but involves different .conf files, which is really painful.
