Team:ZJU-China/model s1 4.htm

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References

 

[1] Yaroslav Chushak, Morley O. Stone. In silico selection of RNA aptamers. Nucl. Acids Res. (2009) 37(12).( http://nar.oxfordjournals.org/content/37/12/e87.short)

 

[2] Florent Barbault. RNA as drug target: docking studies.

 

[3] Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. and Olson, A. J. (2009) Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J. Computational Chemistry, 16: 2785-91.

 

[4] N M O'Boyle, M Banck, C A James, C Morley, T Vandermeersch, and G R Hutchison. "Open Babel: An open chemical toolbox." J. Cheminf. (2011), 3, 33.

 

[5] Hess, et al. (2008) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 4: 435-447.

 

[6] John E. Kerrigan. GROMACS Tutorial for Drug – Enzyme Complex.

 

[7] Justin Lemkul. GROMACS Tutorial: Protein-Ligand Complex. (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html)

 

[8] Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and bond type perception in molecular mechanical calculations". Journal of Molecular Graphics and Modelling , 25, 2006, 247260.

 

[9] Christian E. A. F. Schafmeister, Wilson S. Ross and Vladimir Romanovski, , University of California, San Francisco (1995).

 

[10] Jonikas MA, Radmer RJ, Laederach A, Das R, Pearlman S, Herschlag D, Altman RB. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA. 2009 Feb;15(2):189-99. PMID: 19144906 (2009).

 

[11] M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, V. S. Pande. “Accelerating Molecular Dynamic Simulation on Graphics Processing Units.” J. Comp. Chem., 30(6), 864-872. (2009) (https://simtk.org/home/pyopenmm)

 

[12] Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-38. (http://www.ks.uiuc.edu/Research/vmd/)

 

[13] The PyMOL Molecular Graphics System, Version 1.5.0.4 Schr?dinger, LLC.