Programs

This page provides some programs that can be used in biomolecular dynamic calculation.

Structure-selection

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-selection

Structure-selection is a program that can identify the best combination of bio-molecule conformers from pre-generated conformation pool based on different type of experimental input. The program use a Monte Carlo (MC) simulated annealing method to identify an N-membered ensemble (N can be as few as 1), of which the averaged calculated values should be most consistent with experimental values. To assess the robustness of the method and the convergence of the ensemble structure, the MC simulated annealing is repeated 100 times, each from a randomly selected N-membered ensemble.

 

How to use Structure-selection

Run the program in a Linux system as the following command:

./mc-new.x (experiment file) (calculate file list) (number of MC steps) (number of conformers) (output file)

  • the experiment file should contain two column, one of the residue number and one of the experiment value
  • the calculate file list just need to specifiy the name of the calculated files, which should be pre-calculated before the selection. The calculated file should also contain two column same as the experiment file.
  • The number of MC steps should more than 10 times of the number of calculated files
  • The output file will give the name of selected file, ensemble averaged calculated values and correlation coefficient factor.

Example of output file

Resource files: 
AttachmentSize
Binary Data mc-new.x941.39 KB

DynaXL

As described in the paper

Modeling protein excited-state structures from "over-length" chemical cross-links

Yue-He Ding, Zhou Gong, Xu Dong, Kan Liu, Zhu Liu, Chao Liu, Si-Min He, Meng-Qiu Dong and Chun Tang, J Biol Chem, 292,1187-1196 (2017)

Contact: tanglab@wipm.ac.cn

What is DynaXL

DynaXL lets you to select a local PDB file of your protein, jot down the residues involved in the cross-link and the type of cross-linker. Here each node stands for residue number, and each edge stands for the corresponding crosslinker. You can draw the cross-links you have identified experimentally in any layout. The calculation script will be generated automatically, which can be invoked in Xplor-NIH.

 

How to use DynaXL

Download

The binary file can be freely downloaded here. (upgraded on 18 Nov 2016.) Source code can be found at github.

Install

The program runs on Linux. It depends on X environment and xplor-nihJava version above 1.8 is necessary.

tar xjvf DynaXL.tar.bz2 -C ~/ cd ~/DynaXL chmod a+x ./DynaXL.sh

Run

cd ~/DynaXL ./DynaXL.sh

Tips

  • The program was tested on Ubuntu 16.04 and xplor-nih 2.42. On mac os sierra with xplor-nih 2.42 it seems have some bugs, which may be fixed later,
  • Xplor-nih depends on bc, which is installed by default on most linux distributions, but if your distribution (like ArchLinux dose not ship it by default), please install it by the hand.
  • Make sure that the original PSF file before cross linker patching was generated correctly in the step 2. In this step, we provide two optional way to generate the PSF file. You can choose the “semi-automatically generate the PSF” if your PDB file was in standard format without special amino acids or atoms or residues missing, otherwise, I recommend you to prepare the original PSF file preliminary and select the “choose a PSF file”. If you choose the semi-automatically generate the PSF, please check the PDB file carefully according to the PSF file, especially the ending (see figure below). Sometime the xplor will add an extra oxygen atom for the last residue and rename the last two oxygen atoms as OT1 and OT2 in the PSF file, which will make the inconsistent for the PDB file and PSF file. A simple way to deal with this situation is copy the last line of the PDB file and rename the last two oxygen atoms as OT1 and OT2. 
  • After you draw the topology diagram of cross link and define domains, you can click the step 5 to generate script and run the step 6. The PDB and PSF file with cross linker patched will generated at the beginning of the step 6, you can visualize the PDB file to check whether the cross linker were patched correctly. After that, you can leave the DynaXL away and run the xplor independently. 

Changelog

  • 18 Nov. 2016: add features -- users can define the size of EnsembleSimulation.
  • 13 July 2016: the first public version

sPRE-calc

As described in the paper:

Protein structural ensembles visualized by solvent paramagnetic relaxation enhancement

Zhou Gong, Xin‐Hua GuDa‐Chuan GuoJin 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

Resource files: 
AttachmentSize
Binary Data sPRE.tar.bz2276.35 KB