Coloring and Subcluster Matching

Written by Jiankun Lyu on March 31st, 2021. Modified by Jiankun Lyu on April 12th, 2022.

Automatic way to generate colored matching spheres

Create a directory and copy necessary files from your original receptor preparation folders

set workdir = /where you want to run your coloring and subcluster matching/
mkdir -p ${workdir}
cd ${workdir}
cp /your receptor preparation folder/dockfiles . -r
cp /your receptor preparation folder/INDOCK .
cp /your receptor preparation folder/xtal-lig.pdb .
cp /your receptor preparation folder/working/rec.crg.pdb .
cd dockfiles
$DOCKBASE/proteins/showsphere/doshowsph.csh matching_spheres.sph 1 matching_spheres.pdb

Generate colored matching spheres

cd ../
/nfs/soft/chimera/current/bin/chimera --nogui --script "/mnt/nfs/ex5/work/jklyu/color_matching/scripts/color_matching_spheres.py rec.crg.pdb xtal-lig.pdb dockfiles/matching_spheres.pdb"
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/color_matching_spheres_new.py matching_spheres.cl.sph ./dockfiles/matching_spheres.sph
cp matching_spheres.cl.red.sph dockfiles

The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptors/donors etc represent in different colors; matching_spheres.cl.red.sph is the matching sphere file that can be passed to DOCK3.8 and used in the color matching calculation.

Prepare your INDOCK file for color matching

cp INDOCK INDOCK_cl

The color codes for matching spheres

positive                       (1)
negative                       (2)
acceptor                       (3)
donor                          (4)
ester_o                        (5)
amide_o                        (6)
neutral                        (7)
not_neutral                    (8)
positive_or_donor              (9)
negative_or_acceptor           (10)
neutral_or_acceptor_or_donor   (11)
donacc                         (12)
positive_or_acceptor           (13)
negative_or_donor              (14)
negative_or_acceptor_or_donor  (15)
positive_or_acceptor_or_donor  (16)

The color codes for atoms in the rigid fragment in db2 files

positive                       (1)
negative                       (2)
acceptor                       (3)
donor                          (4)
ester_o                        (5)
amide_o                        (6)
neutral                        (7)

A match in the section below basically define how ligand atoms should match into matching spheres. The first column of a match means the color code from the ligand atom and the second column means the corresponding color code from the matching spheres. For example, a match (1, 1) means that a positive atom (1) from the ligand should be matched onto a matching sphere that is labeled as positive (1).

Add the section below into your INDOCK file

#####################################################
#                             COLORING
chemical_matching            yes
case_sensitive                no
match                         1 1 
match                         2 2
match                         3 3
match                         4 4
match                         5 5
match                         6 6
match                         7 7
match                         1 8
match                         2 8
match                         3 8
match                         4 8
match                         5 8
match                         6 8
match                         1 9
match                         4 9
match                         2 10
match                         3 10
match                         7 11
match                         3 11
match                         4 11
match                         3 12
match                         4 12
match                         1 13
match                         3 13
match                         2 14
match                         4 14
match                         2 15
match                         3 15
match                         4 15
match                         1 16
match                         3 16
match                         4 16
#####################################################

Make sure your INDOCK parameter points to the colored matching spheres

##################################################### 
## INPUT FILES / THINGS THAT CHANGE
receptor_sphere_file          ../dockfiles/matching_spheres.cl.red.sph

Add the section below if you want to explore subcluster matching as well

#####################################################
#                             DOCKING
docking_mode                   4
#####################################################
#               MATCHING
k_clusters          1

Generate colored and clustered matching spheres

Install a conda environment to generate clustered matching spheres

conda env create -f /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/ClusterDOCK.yml

For more information and more analysis scripts, you can find them on Noam's github repo: https://github.com/noamteyssier/ClusterDock

Generate clustered matching spheres

cd ${workdir}
mkdir cluster_spheres
cd cluster_spheres
mkdir meta
cd meta
cp /where you store ligands and decoys/ligands-decoys.sdi enrichment_sdi
cp /where you store ligands and decoys/ligands.name ligands.names
cp /where you store ligands and decoys/decoys.name decoys.names
cp ${workdir}/INDOCK_cl INDOCK
cp ../../dockfiles . -r
cp ../../matching_spheres.cl.red.sph ./dockfiles/matching_spheres.sph
conda activate ClusterDOCK
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {1,2} -n 3 -m
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k 3 -n 5 -m
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {4,5} -n 15 -m
python /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/ClusterDock/src/ClusterSpheres.py -i meta/ -k {6,7} -n 30 -m
conda deactivate

Submit enrichment calculations

cd ${workdir}
python $DOCKBASE/docking/setup/setup_db2_zinc15_file_number.py . ligands-decoys_ ligands-decoys.sdi 20 count
cp /where you store ligands and decoys/ligands-decoys.sdi .
cp /where you store ligands and decoys/ligands.name ligands.names
cp /where you store ligands and decoys/decoys.name decoys.names
csh /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/colored_subcluster_docking/submit.csh ${workdir} ${workdir}/cluster_spheres/

Analyze your enrichment calculations

cp /mnt/nfs/ex4/work/jklyu/colored_subcluster_matching/scripts/analysis.csh ${workdir}
# You have to tweak the analysis script to run on your own system, because the script is designed for running DUDE benchmark on this method
# I will revisit this part when I have time
csh analysis.csh