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PreprintCC BYChemRxiv

RaX-DT: An Open-Source Platform for Automated Molecular Docking Workflows and Reproducible Pipeline Validation

  • Amir Hosein Ghavi1,2
  • Bita Barazandeh Shirvan1,2
  • Zohre Ganji3,2
  • Zahra Jafari1,2
  • Mojgan Nejabat4,2
  • Farzin Hadizadeh5,2,6
  • Narges Hashemi1,2,6
  • Javad Akhondian1,2,7
  • Farah Ashrafzadeh1,2,7
  • Farnoosh Ebrahimzadeh7,2
  • Mohammad Javad Jafari7,2,8,9
  • Mehran Beiraghi Toosi1,2,6
9 affiliations
  1. 1Rare Pediatric Neurological Diseases Research Center
  2. 2Mashhad University of Medical Sciences
  3. 3Basic Sciences Research Institute
  4. 4School of Pharmacy
  5. 5Pharmaceutical Technology Institute
  6. 6Neuroscience Research Center
  7. 7Faculty of Medicine
  8. 8Faculty of Veterinary Medicine
  9. 9Shab.C., Islamic Azad University
Open at sourcePDFDOICite

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.

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Cite

BibTeXRIS
BibTeX
@misc{ghavi2026raxdt,
  title = {{RaX-DT: An Open-Source Platform for Automated Molecular Docking Workflows and Reproducible Pipeline Validation}},
  author = {Amir Hosein Ghavi and Bita Barazandeh Shirvan and Zohre Ganji and Zahra Jafari and Mojgan Nejabat and Farzin Hadizadeh and Narges Hashemi and Javad Akhondian and Farah Ashrafzadeh and Farnoosh Ebrahimzadeh and Mohammad Javad Jafari and Mehran Beiraghi Toosi},
  howpublished = {ChemRxiv},
  year = {2026},
  month = sep,
  doi = {10.26434/chemrxiv.15009171/v1},
  url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009171/v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - RaX-DT: An Open-Source Platform for Automated Molecular Docking Workflows and Reproducible Pipeline Validation
AU  - Amir Hosein Ghavi
AU  - Bita Barazandeh Shirvan
AU  - Zohre Ganji
AU  - Zahra Jafari
AU  - Mojgan Nejabat
AU  - Farzin Hadizadeh
AU  - Narges Hashemi
AU  - Javad Akhondian
AU  - Farah Ashrafzadeh
AU  - Farnoosh Ebrahimzadeh
AU  - Mohammad Javad Jafari
AU  - Mehran Beiraghi Toosi
PY  - 2026
DA  - 2026/09/21
PB  - ChemRxiv
DO  - 10.26434/chemrxiv.15009171/v1
UR  - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009171/v1
AB  - 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.
ER  -