Skip to content

Latest commit

 

History

History
33 lines (20 loc) · 1.18 KB

README.md

File metadata and controls

33 lines (20 loc) · 1.18 KB
Raw

oligonucleotides-kinetics

IPython notebooks for the Markov state models analysis of molecular dynamics simulations of RNA di-, tri-, and tetra-nucleotides.

Content

  • dinucleotides.ipynb contains the analysis of the 8 dinucleotide systems (AC, CA, CC, AA at T=300K,277K);
  • trinucleotide.ipynb contains the analysis the trinucleotide AAA (T=300K)
  • tetranucleotide.ipynb contains the analysis of the tetranucleotide AAAA (T=275K)
  • .py files are included, containing various scripts and functions used in the notebooks for the analysis.

Data download

Molecular dynamics trajectories can be downloaded from the following link https://goo.gl/2HcQ5L

Reference

The results of this analysis have been published in

Pinamonti, G., Zhao, J., Condon, D.E., Paul, F., Noe, F., Turner, D.H., and Bussi, G., "Studying the kinetic properties of RNA oligonucleotides with Markov state models", J. Chem. Theory Comput., 2017, 13 (2), pp 926–934

Please cite this paper if you use any part of this material

Software requirements

  1. Python 2.7

  2. Jupyter Notebook http://jupyter.org/

  3. PyEMMA 2.2.6 http://www.emma-project.org/v2.2.6/