Author: Shinji Iida
- MDAnalysis >= 1.0.0 (https://www.mdanalysis.org/)
- mdtraj >= 1.9.4 (https://www.mdtraj.org/1.9.4/index.html#)
- pandas >= 1.1.3
- python >= 3.6
export PATH=${PATH}:path_to_/crypticSitePredictor/src
$ crypticSitePredictor.py -h
usage: crypticSitePredictor.py [-h] -r REF -i TRJ [-o OUT] [-a ALPHA] [-b BETA] [-th THRESHOLD] [-tr TRJ_RANGE [TRJ_RANGE ...]]
This is Cryptic-site predictor
optional arguments:
-h, --help show this help message and exit
-r REF, --ref REF
-i TRJ, --trj TRJ
-o OUT, --out OUT output suffix
-a ALPHA, --alpha ALPHA
Upper bound of Delta F
-b BETA, --beta BETA Lower bound of sigma
-th THRESHOLD, --threshold THRESHOLD
threshold
-tr TRJ_RANGE [TRJ_RANGE ...], --trj_range TRJ_RANGE [TRJ_RANGE ...]
traj range
- More than 5 independent canonical MD simulations more than 500 ns are preferable for the prediction.
- Input trajectories are assumed to have no hydrogen atom.
- Golden section spiral algorithm calcuates Solvent Accessible Surface Area per residue
Please cite: https://dx.doi.org/10.1021/acs.jpcb.0c04963