script for structure refinement against solvent PRE

  • Posted on: 13 March 2018
  • By: gongzhou

As described in the paper:

 Theory and practice of using solvent paramagnetic relaxtion enhancement to characterize protein conformational dynamics

Zhou Gong, Charles D.Schwieters, ChunTang,  Methods, 148:48-56 (2018)

 Contact: tanglab@wipm.ac.cn

 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.

Resource files: 
AttachmentSize
Package icon sPRE-refine.zip1.49 KB