RaX-DT: An Open-Source Platform for Automated Molecular Docking Workflows and Reproducible Pipeline Validation
Year: 2026
Type: preprint
Abstract: Automated molecular docking workflows often fail not at the scoring engine but at the interfaces between ligand preparation, protein preparation, binding-site definition, and post-processing. We present RaX-DT, an open-source, Docker Compose–deployable platform that integrates these steps in a single web application and an optional conversational assistant. RaX-DT automates 3D ligand generation, tautomer/protonation-state handling, protein cleaning, binding-site definition via P2Rank, Fpocket, or user-specified coordinates, GNINA-based docking, and interactive result visualization. Because end-to-end automation can introduce silent failures, we validated the assembled workflow on 231 protein–ligand co-crystal structures from DUD-E and LIT-PCBA rather than treating the docking engine in isolation. Of these, 186 structures completed successfully; the top-ranked pose reproduced the crystallographic pose within 2.0 Å for 65.1% of completed structures, and the best of the five top-scoring poses reached 77.4%. Validation also exposed a box-placement defect that would have produced plausible-looking but invalid output, underscoring the value of pipeline-level quality control. RaX-DT is released under the MIT license and is intended to improve accessibility, reproducibility, and transparency in routine docking workflows.
Source: ChemRxiv
Language: English
Subfield: Drug Discovery
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7213945691