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: [email protected]
Date: Sept 27, 2020
Linux/Unix
gcc compiler >4.8 version
To make RLDOCK, type:
cd RLDOCK
bash install.shIf make installed, just type:
cd RLDOCK
make-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 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).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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