DOCKovalent linker design tutoral

This was written on April 4, 2018.

This tutorial is for designing linkers for a covalent inhibitor and is supplement the work in preparation (Wan et al 2018).

These file are in the /mnt/nfs/home/xiaobo/UCSF_scripts/2018-4-3-covlanet_lysine_wiki-tutorial

Step 1. Custom Ligand and Library Generation

1/Custom Ligand / Library Generation

cd 1-Custom-Ligand-Library-Generation

For meta-SF library building

reaction1:

python step1-reaction-amines-Br.py scaffod.smi 817.zinc.list.smi
                       scaffod.smi is the smile of the scaffold for reaction
                       817.zinc.list.smi is the smile of collecte 817 different diamine linkers

reaction2:

python step2-reaction-SF-meta.py scaffold.ism
                       inputfile: scaffold.ism is the primary products without the SF
                       outputfile: final_scaffold1.smi

reaction3: remove the doubles

python step3-remove_doubles.py final_scaffold1.smi
                       inputfile:final_scaffold1.smi
                       outputfile: no_doubles_out.ism

The no_double_out.ism was used to generate db2 file for covalent docking log into gimel

setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7-beta9-min
setenv DOCKBASE /mnt/nfs/home/xiaobo/combine_docknormal_dock_covalent_3.7_and_tart/DOCK_from_githup_2016_5_27
/nfs/soft/tools/utils/qsub-slice/qsub-mr-meta -tc 50 --map-instance-script "/nfs/soft/tools/utils/qsub-slice/qsub-mr-map.sh" -s $BUILD_ENVIRONMENT -l 1 no_doubles_out.ism $DOCKBASE/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent

Step 2 Protein preparation (different lysine rotamers)

2/Protein preparation (different lysine rotamers)

cd 2-Protein-preparation-different-lysine-rotamers

find the modification lys number in the PDB

echo "5K9I-B-X44      B       295">>lys.list
bash step0_prepare_build_system.sh  5K9I-B-X44

in the window of chimera, select all of the 27 lysine rotamers and click the button of OK. Reselect all the lysine rotamers in the PDB structure, and the save to PDB format LYS-5K9I-B-X44.pdb Then, to generate all 28 structure folds, and then automatically calculate the steric clash with nearby residues, and select the rotamer with no steric clashes. This scripts will also calculate the nearest atom of in the compound to the lysine NZ atom

bash step1_run_build_system.sh 5K9I-B-X44 
5K9E-B-X44      SBH     2.038
5K9B-B-X44      SBH     2.321
5K9I-B-X44      OBI     2.949
5K9L-B-X44      SBH     4.683
5K9R-B-X44      OBI     4.925

Each folder contains rec.pdb and xtal-lig.pdb

For each folder

bash step1_DOCKINV.blastermaster.sh 5K9I-B-X44 box_margin(10) 1(covalent docking)

box_margin is defined from the center of the xtal-lig.pdb file