script for structure refinement against solvent PRE
As described in the paper:
Theory and practice of using solvent paramagnetic relaxtion enhancement to characterize protein conformational dynamics
What is structure refinement using sPRE data
Here, we provide Xplor-NIH scripts of structure refinement using solvent PRE data for GB1 protein.
The scripts using PSolPot potential to refine the structure against solvent PRE data.
A PSolPot term has been introduced in the Xplor-NIH structure calculation program (release 2.46 or later), which allows the direct structure refinement against the sPRE data. Covering the cosolute-excluded protein surface with tessellation, the surface integral approach does not have the problem encountered by the first approach employing raw atom-grid distances with 0 or 1 contribution from each grid point.
How to use structure refinement using sPRE data
The refinement scripts using Xplor-NIH to perform the ensemble structure refinement calculations. Thus, the Xplor-NIH (version 2.46 or later) should be pre-installed. The PDB file, PSF file, restraint file including solvent PRE value should prepared before the calculation. The script can be run by the following command
xplor -py sPRE-refine.py
These scripts can be easily modified for ensemble structure refinement for the other protein or nucleic acid systems.