Covalent library preparation 2023

Modify warhead to covalent adduct with SiH3 added.

Prepare “SMILES ID” file.

ssh n-1-17 (or another development node)

Source environment with RDkit

source /mnt/nfs/ex9/work/ttummino/miniconda/etc/profile.d/conda.sh

conda activate base3.7

python ~ak87/PROGRAM/convert_smiles_to_covalent.py ald bbv-cov-ald.smi bbv-cov-ald-test.smi

This script enumerates all stereoisomers and converts SMILES to the covalent ones. Currently, only conversions for aldehydes and nitriles is supported. Usage:

• First arg: ald or nitr for aldehyde or nitrile

• Second arg: input smi file

• Third arg: output file name

Preparing ligands

Prepare smiles with aldehyde converted to OH, and SiH3 attached off of the aldehyde Carbon

1. to convert ChemSpace SMILES to normal

awk -F"\t"  '{print $1, $2}' 2021q1-2_Enamine_REAL_Covalent_ArOSO2F_66.7K_CXSMILES.cxsmiles | sed '1,$ s/[|][&0-9:,a-z]*[|]//g'> 2021q1_2_Enamine_REAL_Covalent_ArOSO2F_66.7K_CXSMILES.smi

setenv DOCKBASE  /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1
setenv BUILD_ENVIRONMENT /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/env.sh
/nfs/soft/tools/utils/qsub-slice/qsub-mr-meta -tc 1000 --map-instance-script "/nfs/soft/tools/utils/qsub-slice/qsub-mr-map.sh" -s $BUILD_ENVIRONMENT -l 100 <NAME>.smi $DOCKBASE/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent