Team:EPF-Lausanne/Information & references

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===LOV2 & LOVTAP references===
===LOV2 & LOVTAP references===
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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]]
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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]])
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# 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])
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# 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 Article])
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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])
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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])
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# 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])
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# 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])
===VMD informations===
===VMD informations===

Revision as of 15:16, 19 October 2009

Contents

Information and references



LOV2 & LOVTAP references

  1. 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)
  2. 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)
  3. 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)
  4. 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)

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.


Run a simulation

A simulation is composed of different steps. Here are a few links that deal with heating and stabilization.


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