ligand-preparation

LigandForge is a modular ligand preparation and virtual screening pipeline for drug discovery that integrates ADMET filtering, 3D conformer generation, Meeko-based ligand preparation, and AutoDock Vina docking—with full provenance tracking, checkpointing, and clean restarts.

Protein Ligand Abstraction and Hydrogenization tool. A cheminformatic tool that separate protein and ligand from the PDB file, fix the bond order of the ligand, protonate protein and ligand separately, then write them to separate file.

This repository provides a comprehensive module on structural biology and drug discovery, covering protein structure, docking, and drug design. It runs on Google Cloud Platform using Jupyter notebooks and includes tools like PyMOL and AutoDock.

End-to-end, config-driven workflows (RDKit, Open Babel, Vina, PLIP, PyMOL/ChimeraX) with reproducible seeds and clean outputs.

Automated Windows pipeline that protonates ligand PDB files at pH 7.4 and converts them in bulk to AutoDock-ready PDBQT format using Open Babel 3 + MGLTools

Generates an SDF conformer ensemble from SMILES. This script creates an initial pool of 250 conformers (using RDKit ETKDG), optimizes them (MMFF94), and then applies a greedy diversity filter. The final ensemble contains a subset of conformers selected for both their low energy and geometric diversity (RMSD threshold).