2022_sbdd_practice

sbdd practice files for 2022 workshop

Set environment

$ conda create -n sbdd_practice python=3.7
$ conda activate sbdd_practice
$ conda config --env --add channels conda-forge
$ conda install -c conda-forge numpy swig boost-cpp sphinx sphinx_rtd_theme scipy rdkit openmm openbabel pdbfixer pymol-open-source
$ pip install vina meeko

Practice Summary

Download from PDB

PDB ID: 6W63, 7VTH, 7VU6

Download PDB files from the PDB website https://www.rcsb.org/

or

$ wget https://files.rcsb.org/download/6W63.pdb

1. Re-docking

Receptor - 3CL protease (PDB ID: 6w63)
Ligand - 3CL protease inhibitor X77 (PDB ID: 6w63)

$ python pdb_prep.py
$ python lig_prep.py
$ python get_box.py
$ python simple_run.py
$ pymol *.pdbqt

Analysis docking model wih PyMol
Run below command in PyMol

rms /ligand////*, /ligand_vina_out////*
split_states ligand_vina_out
rms /ligand////*,/ligand_vina_out_0001////*

2. Docking ligands to receptor (PDB ID: 6w63)

$ python run_docking.py
$ pymol pdb/7vth.pdb pdb/7vu6.pdb receptor.pdbqt *_vina_out.pdbqt

Run below command in PyMol

align 7vu6, receptor
align 7vth, receptor