molclaw-quickvina-docking

What problem does it solve?

Automates end-to-end molecular docking between a prepared protein structure and small-molecule ligands using QuickVina2-GPU to produce binding affinity estimates and pose files for downstream analysis and ranking.

Core Features & Use Cases

• Integrated multi-step workflow: orchestrates protein retrieval, chain extraction, structure repair, pocket detection, format conversions, and GPU-accelerated docking into a single reproducible pipeline.
• Robust validation and guardrails: enforces a minimum 25 Å box per axis, checks for negative and reasonable affinity scores, performs progressive box enlargement retries, and ensures mandatory pose file download for downstream rescoring.
• Practical use cases: high-throughput virtual screening to prioritize hits, per-ligand docking for lead optimization, and reproducible docking steps in benchmarked evaluation pipelines.

Quick Start

Run molclaw-quickvina-docking to dock a list of SMILES-derived ligands against a prepared protein structure, return affinity values, and save pose PDBQT files.