elelab / g_reff Goto Github PK

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

This repository includes scripts to back-calculate NOEs from biomolecular ensembles, such as the ones obtained by a MD simulation, as well as to compare to a set of experimental ones.
It contains two python scripts:
1.  NOEconverter.py which helps in the creation of the right file format for the experimental data
2. g_reff to carry out the calculation of NOEs from the ensemble, as well as to compare with the experimental NOEs. 

usage: g_reff [-h] -r NOES [-p PDB]

Calculate Reff on selected atom classes from an MD simulation

optional arguments:
  -h, --help            show this help message and exit
  -r NOES, --reff NOES  noes file
  -p PDB, --pdb PDB     pdb file

EXAMPLE

An example is provided in this repository with a short trajectory to test the tool.
The first step is the conversion to the proper NOE format using as input: i) the first frame of the ensemble, for example First_frame_chain_A.pdb, as a reference pdb file; ii) the file with the experimental NOEs from the BMRB database; iii) a conversion table for the atom name compatible with the force field used in the simulation (in the example CHARMM) 

python NOEconverter.py -pdb First_frame_chain_A.pdb -noe BMRB_NOE.mr -c AAtable_new_CHARMM.par

This step generates a .dat file that can be used by g_reff

The second step is the calculation of the NOEs from the ensemble and its comparison with the experimental data 

python2.7 g_reff -r NOE_converted.dat -p trajectory.pdb 

When using the g_reff and NOEconverter.py for publication 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.