sPRE-calc

As described in the paper:

Protein structural ensembles visualized by solvent paramagnetic relaxation enhancement

Zhou Gong, Xin‐Hua Gu, Da‐Chuan Guo, Jin Wang and Chun Tang,  Angew Chem Int Ed, 56,1002-1006

 Contact: tanglab@wipm.ac.cn

What is sPRE-calc

sPRE-calc is a fortran program to calculate the theoretical value of solvent PRE using grid model approach. The solvent effect for a proton is integrated over all the grid points, as defined in the following equation.

Here, the ωl,m,n has a value of 1 if the paramagnetic probe is allowed for grid point (l, m, n), and 0 for excluded points taken up by the molecule.

How to use sPRE-calc

Install : tar xjvf sPRE.tar.bz2; chmod a+x sPRE.x

Usage : ./sPRE.x (pdb file) (Rprobe) (Dpara) (Atom)

Rprobe: the size of paramagnetic probe

Dpara : the concentricity of paramagnetic center, 0 means right at the center

Atom : the name of atom used for sPRE calculation, which will list in the third column of the output. 'HM' represents protons of methyl group

Example of output file