Published November 14, 2025 | Version This version includes an improved release of the jamlib program previously provided in Version 1. Users are encouraged to use this updated version for the best and most up-to-date functionalities.
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A collection of bash scripts for a virtual screening pipeline: from compound library generation to docking score evaluation

Authors/Creators

  • 1. EDMO icon University of Cantabria

Description

This resource includes five bash scripts designed to simplify and automate key stages of a virtual screening pipeline, making molecular docking more accessible to non-experts. The scripts facilitate compound library preparation, receptor setup, automated docking, job resumption, and docking result analysis, using tools such as QuickVina 2 (AutoDock Vina), OpenBabel, AutoDockTools and fpocket.

The scripts included are:
1.    jamlib – Automatically generates compound libraries in PDBQT format, including FDA-approved drugs and custom libraries of purchasable compounds, ready for use with QuickVina 2. Important note: This program downloads compounds from the free ZINC database (zinc.docking.org), provided by the Irwin and Shoichet Laboratories, and from files.docking.org and files2.docking.org. According to the original license from files.docking.org: "Whereas you are free to share results derived from the use of these files, you may not redistribute major portions without the express written permission of John Irwin: chemistry4biology at gmail dot com". Therefore, the compound libraries generated by this program are for PERSONAL, ACADEMIC, and NON-COMMERCIAL use only. Redistribution or sharing of these files with third parties is LIMITED and must fully comply with the original license terms.
2.    jamreceptor – Prepares receptor structures (in PDB format) by converting them to PDBQT, identifying binding pockets using fpocket, and generating grid box configuration files.
3.    jamqvina – Automates the setup and execution of docking jobs with QuickVina 2, including parameter configuration and time estimation.
4.    jamresume – Enables the resumption of interrupted docking jobs, whether due to planned pauses or unexpected failures.
5.    jamrank – Provides two modes for analyzing docking results: 
             o    A fast mode that outputs affinities, ZINC links, and compound IDs.
             o    A detailed mode that additionally computes a similarity score among poses, molecular weight, number of poses, and generates a comprehensive summary.

This toolkit is intended to assist researchers in drug discovery projects by streamlining repetitive tasks and reducing the barrier to performing molecular docking experiments.

Files

README.txt

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Additional details

Funding

Fundação para a Ciência e Tecnologia
CANDIGLUE - Molecular glues as new fungicides against Candida albicans 2023.13395.PEX

Software

Repository URL
https://github.com/jamanso/jamdock-suite
Programming language
Shell

References

  • Manso, J.A. (2025). A collection of bash scripts for a virtual screening pipeline: from compound library generation to docking score evaluation. Zenodo, https://doi.org/10.5281/zenodo.15577778.
  • O'Boyle, N.M., Banck, M., James, C.A., Morley, C., Vandermeersch, T., and Hutchison, G.R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics 3, 33. https://doi.org/10.1186/1758-2946-3-33.
  • Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R.K., Goodsell, D.S., and Olson, A.J. (2009). AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility. J Comput Chem 30, 2785–2791. https://doi.org/10.1002/jcc.21256.
  • Le Guilloux, V., Schmidtke, P., and Tuffery, P. (2009). Fpocket: An open source platform for ligand pocket detection. BMC Bioinformatics 10, 168. https://doi.org/10.1186/1471-2105-10-168.
  • Trott, O., and Olson, A.J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry 31, 455–461. https://doi.org/10.1002/jcc.21334.
  • Alhossary, A., Handoko, S.D., Mu, Y., and Kwoh, C.-K. (2015). Fast, accurate, and reliable molecular docking with QuickVina 2. Bioinformatics 31, 2214–2216. https://doi.org/10.1093/bioinformatics/btv082.
  • Irwin, J.J., and Shoichet, B.K. (2005). ZINC − A Free Database of Commercially Available Compounds for Virtual Screening. J. Chem. Inf. Model. 45, 177–182. https://doi.org/10.1021/ci049714+
  • Sterling, T., and Irwin, J.J. (2015). ZINC 15 – Ligand Discovery for Everyone. J. Chem. Inf. Model. 55, 2324-2337. https://doi.org/10.1021/acs.jcim.5b00559
  • Irwin et al. (2020). ZINC20—A Free Ultralarge-Scale Chemical Database for Ligand Discovery. J. Chem. Inf. Model. 60, 6065–6073. https://doi.org/10.1021/acs.jcim.0c00675.