TIS2AA

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Requirements:

• Numpy
• Fortran compiler
• For minimization, AmberTools (https://ambermd.org/AmberTools.php) is required.

Getting started

1. Clone the repository including submodules.

$ git clone --recurse-submodule https://github.com/naotohori/TIS2AA 

If you already have this repository without submodules, use the following command inside the directory.

$ git submodule update --init

2. Library preparation.

$ cd TIS2AA/bin/fQCP
$ make f2py
$ cd ../..

A shared object CalcROT.cpython-XX-XXXX.so will be created.

3. Download fragment libraries

$ curl -L https://www.dropbox.com/s/uuiif7di6vg8wex/RNA09_FRAG.tar.gz | tar zx
$ curl -L https://www.dropbox.com/s/n8j5smkxp09ace9/DNA_FRAG.tar.gz | tar zx

Usage

 $ TIS2AA/bin/tis2aa.py  trna.cg.pdb  trna.log trna.aa.pdb
 $ TIS2AA/bin/min.py  trna.aa.pdb  trna.aa.min.pdb

For DNA, add --model TISDNA as follows.

$ .TIS2AA/bin/tis2aa.py --model TISDNA 1wqz.cg.pdb 1wqz.aa.pdb

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References

1. Murray, L. J. W., Arendall, W. B., Richardson, D. C., & Richardson, J. S. (2003). RNA backbone is rotameric. Proceedings of the National Academy of Sciences, 100(24), 13904–13909. http://doi.org/10.1073/pnas.1835769100
2. Humphris-Narayanan, E., & Pyle, A. M. (2012). Discrete RNA Libraries from Pseudo-Torsional Space. Journal of Molecular Biology, 421(1), 6–26. http://doi.org/10.1016/j.jmb.2012.03.002