Team:EPF-Lausanne/Information & 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.

• 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.