cheminformatics

Perform operations on chemical structures using Python.

Introduction

pdb_ligand_id-to-smi.ipynb notebook demonstrates how to obtain SMILES of ligands using ligand ID from PDB.

ligand-id-to-str-in-pdb-format.ipynb will download 3D ligand structures from PDB in SDF format and then will convert them into PDB format.

sdftosmi.py script will convert molecules in sdf format into their corresponding SMILES. All molecules are provided in a single SDF file as input.

smitostr.py will convert smiles to structure.

swarm-plot.ipynb plots swarm boxplot of docking score of ligands.

Requirements

It requires Python3. This script uses RDKit and some additional packages. Install them using the following commands.

conda create -c conda-forge -n my-rdkit-env rdkit

conda install pandas

Usage

To get SMILES and/or structures from ligand IDs, save all ligand IDs in a CSV file (lig-ids.csv) and run the notebook(s). The other two scripts are simple Python scripts that you can easily run in a terminal.

For more information, read this article: https://bioinformaticsreview.com/20221120/how-to-obtain-smiles-of-ligands-using-pdb-ligand-ids/