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Team:TU Darmstadt/Materials/Software
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<li><a href="/Team:TU_Darmstadt/Downloads" title="Downloads">Downloads</a></li></ul></li> | <li><a href="/Team:TU_Darmstadt/Downloads" title="Downloads">Downloads</a></li></ul></li> | ||
| - | <li><a href="/Team:TU_Darmstadt/Human_Practice" title="Human Practice">Human Practice</a | + | <li><a href="/Team:TU_Darmstadt/Human_Practice" title="Human Practice">Human Practice</a></li> |
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<li><a href="/Team:TU_Darmstadt/Sponsors" title="Sponsors">Sponsors</a><ul> | <li><a href="/Team:TU_Darmstadt/Sponsors" title="Sponsors">Sponsors</a><ul> | ||
<li><a href="/Team:TU_Darmstadt/Sponsors" title="Sponsors">Overview</a></li> | <li><a href="/Team:TU_Darmstadt/Sponsors" title="Sponsors">Overview</a></li> | ||
Latest revision as of 20:45, 26 September 2012
Software
Visualistaion
- Molecular Graphic and animations we used yasara:
Krieger, E., Koraimann, G., & Vriend, G. (2002). Increasing the precision of comparative model with YASARA NOVA--a self-parameterizing force field. Proteins, 47(3), 393-402. Wiley Online Library. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/11948792
- Molecular Graphic for the Information Theory we used [http://www.ks.uiuc.edu/Research/vmd/ vmd] :
Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38.
- Molecular Graphic for homology modeling we used Chimera :
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem, 25(13), 1605-1612. doi:10.1002/jcc.20084
Computation
- For plots and calculations we use [http://www.r-project.org R] :
Team, R. D. C. (2008). R: A Language and Environment for Statistical Computing. Vienna, Austria.
- For the GNM calculations we used :
Hoffgaard, F., Weil, P., & Hamacher, K. (2010). BioPhysConnectoR: Connecting sequence information and biophysical models. BMC Bioinformatics, 11, 199. doi:10.1186/1471-2105-11-199
- For alignment creation we used Clustal omega
Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., et al. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7(539), 539. Nature Publishing Group. doi:10.1038/msb.2011.75
- For the sequnece search we used BLAST:
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25(17), 3389-3402.
- For molecular dynamics we used Yasara:
Krieger, E., Koraimann, G., & Vriend, G. (2002). Increasing the precision of comparative model with YASARA NOVA--a self-parameterizing force field. Proteins, 47(3), 393-402. Wiley Online Library. [http://www.ncbi.nlm.nih.gov/pubmed/11948792 link]
- For docking simulation :
Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK and Olson AJ (1998), J.Comput.Chem. 19, 1639-1662
