Covalent Library Preparation 2024

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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

SSH Gimel 

ssh gimel

Set to csh 

csh

Source Environments 

source ~elisfink/.csh_corina
setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk
source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh

Run Script with input.smi as your prepared SMILES file 

csh ~elisfink/scripts/09-2022-ligbuild/0001_wrapper_queue_build_smiles_ligand_mod_corina_covalent.csh input.smi
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