RLDOCK is a open source program for predicting the RNA-ligand binding site and binding pose. Author: Li-Zhen Sun, Yangwei Jiang, Yuanzhe Zhou, & Shi-Jie Chen Email: [email protected] Date: Sept 27, 2020
Linux/Unix gcc compiler >4.8 version
To make RLDOCK, type:
cd RLDOCK
bash install.shor, if make installed, just type:
cd RLDOCK
makeThe executable file RLDOCK will be saved in the bin folder.
-i <receptor.mol2> # an RNA file in MOL2 format
-l <ligand.mol2> # a ligand conformer file in MOL2 format
-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 of 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) Mol2 file of the ligand for RMSD calculation
# if this file is not available, the first input conformer of the ligand will be set as the conformer for RMSD calculation
-b <center_x,center_y,center_z,size_x,size_y,size_z> # (optional) specify the center and the size of the docking box in Å, values separated by comma and no space between each value.
# each size_x/y/z measures the whole side length of the box in the corresponding x/y/z directionWe 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.mol2There 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_SF_low.mol2 # Record the poses of XXX_SF_low.dat in mol2 format
XXX_SF_high.mol2 # Record the poses of XXX_SF_high.dat in mol2 format
XXX_cluster.mol2 # Top poses (default 10 poses) after clustering.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.
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