RLDOCK

RLDOCK is a source-availabe program for predicting the binding site and binding pose for ligand-RNA binding.
Author: Li-Zhen Sun, Yangwei Jiang, Yuanzhe Zhou, & Shi-Jie Chen
Email: chenshi@missouri.edu
Date: Sept 27, 2020

System Requirement

Linux/Unix
gcc compiler >4.8 version

Compilation

To make RLDOCK, type:

cd RLDOCK  
bash install.sh

If make installed, just type:

cd RLDOCK  
make

Command line options

-i <receptor.mol2>  # an RNA file in the format of MOL2  
-l <ligand.mol2>    # a ligand conformer file in the format of MOL2  
-o <output prefix>  # path and filename for output files  
-n <thread number>  # number of threads used for simulation  
-r <reference ligand file>  # (optional)the Mol2 file of the ligand for RMSD calculation.  

We recommend using Chimera and Open Babel to generate related files.
Important Note: The order of atoms in <reference ligand file> should be the same as the order in <ligand.mol2>.

example:

 ./RLDOCK -i job1_RNA.mol2 -l job1_ligand.mol2 -o job1 -n 20 -r job1_ref_lig.mol2    

Output files

There will be 4 output files for each simulation:

XXX_pocket.dat  # Record the information of potential binding sites.  
XXX_usepose.dat # Record the information of selected poses for scoring step.  
XXX_SF_low.dat  # Record the scoring and ranking information by using the low resolution scoring function(SF-l).  
XXX_SF_high.dat # Record the scoring and ranking information by using the high resolution scoring function(SF-h).

Example

The necessary files for the example cases are in the file Example. To run the example cases, type:

 cd RLDOCK
 bash run_3GCA.sh # An example with 0 rotatable bond.  
 bash run_3F2T.sh # An example with 7 rotatable bonds.