Team:TU Darmstadt/Materials/Software

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 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 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. 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