elelab / csx2-cross-validation Goto Github PK

Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark

CSX2.py can be used to compare chemical shifts calculated from simulated ensemble of structures with experimental chemical shifts from NMRspectroscopy.
A guide to the script's options is available running:
python CSX2.py -h

This script calculates X^2 values based on experimental values and predicted values.
Chisquare is calculated as:

     ((CS_pred - CS_exp)**2)/(CS_exp) 

where CS_pred is the cummulative average predicted chemical shifts and CS_exp is the experimentally obtained chemical shifts.
Predictors can be carried out with PPM (old version, needs pre-run of ppm_linux generating proton_details.dat and bb_details.dat files (recommended for first run)). 
PPM_One new version (ppm_linux need to be executable in the same folder of the pdb file example.pdb).

In this repository and example is provided with a pdb file (example.pdb) and the corresponding experimental CS (ChemicalShifts.dat).

When using the CSX2.py for publication or presentation please cite:

Matteo Lambrughi, Matteo Tiberti, Maria Francesca Allega, Valentina Sora, Mads Nygaard, Agota Toth, Juan Salamanca Viloria, Emmanuelle Bignon, Elena Papaleo*, Analyzing biomolecular ensembles.
Methods Mol Biol. 2019;2022:415-451. doi: 10.1007/978-1-4939-9608-7_18.