EtienneReboul/RLDOCK

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

or, if make installed, just type:

cd RLDOCK  
make

Executable file

The executable file is RLDOCK in the base folder.

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  
-c <number of output poses>  # number of output poses after clustering (if this number is larger than number of clusters, the number output poses will be same as the number of clusters)
-n <thread number>  # number of threads used for simulation  
-s <path of sphere.dat>  # sphere.dat records shafts used for rotating ligands and  is stored in `src`
-r <reference ligand file>  # (optional)the Mol2 file of the ligand for RMSD calculation
                            # if the file is not available, the first input conformer of ligand will be set as the conformer 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 -c 10 -n 20 -s src/sphere.dat -r job1_ref_lig.mol2

Output files

There will be 6 output files for each simulation. .xyz and .mol2 are for visualization. :

XXX_pocket.dat  # Record the geometric score for potential binding sites.  
XXX_pocket.xyz  # Potential binding sites are recorded in the format of .xyz for visualization.
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).
XXX_cluster.mol2 # Top poses (default 10 poses) after clustering.

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.

EtienneReboul / RLDOCK