How to cite ChemServer

Cite ChemServer

Use this reference and add the date you used the service:

ChemServer: free online molecular docking and computational chemistry. Available at https://chemserver.online (accessed [date]).

The same reference for LaTeX:

@misc{chemserver,
  author       = {{ChemServer}},
  title        = {ChemServer: free online molecular docking and computational chemistry},
  year         = {2026},
  howpublished = {\url{https://chemserver.online}},
  note         = {Accessed [date]}
}

Download it as BibTeX or as RIS for Zotero, Mendeley and EndNote.

Cite the programs your run used

ChemServer runs established open source programs, and their authors deserve the credit for the science. The file METHODS_AND_CITATIONS.txt in every docking download lists the programs, versions and references of that run. These are the main ones:

• AutoDock Vina 1.2. Eberhardt J, Santos-Martins D, Tillack AF, Forli S. AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings. J Chem Inf Model. 2021;61(8):3891-3898. doi:10.1021/acs.jcim.1c00203
• AutoDock Vina. Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455-461. doi:10.1002/jcc.21334
• AutoDockTools (MGLTools). Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785-2791. doi:10.1002/jcc.21256
• Meeko. Meeko (Forli Lab, Scripps Research), https://github.com/forlilab/Meeko, described in Eberhardt J, et al. J Chem Inf Model. 2021;61(8):3891-3898. doi:10.1021/acs.jcim.1c00203
• Open Babel. O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminform. 2011;3:33. doi:10.1186/1758-2946-3-33
• RDKit. RDKit: Open-source cheminformatics, https://www.rdkit.org
• Vina-GPU 2.1. Tang S, Ding J, Zhu X, Wang Z, Zhao H, Wu J. Vina-GPU 2.1: towards further optimizing docking speed and precision of AutoDock Vina and its derivatives. IEEE/ACM Trans Comput Biol Bioinform. 2024. doi:10.1109/TCBB.2024.3467127
• GNINA. McNutt AT, Francoeur P, Aggarwal R, Masuda T, Meli R, Ragoza M, Sunseri J, Koes DR. GNINA 1.0: molecular docking with deep learning. J Cheminform. 2021;13:43. doi:10.1186/s13321-021-00522-2
• PDBFixer and OpenMM. Eastman P, et al. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. J Phys Chem B. 2024;128(1):109-116. doi:10.1021/acs.jpcb.3c06662 (PDBFixer)
• MODELLER. Webb B, Sali A. Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics. 2016;54:5.6.1-5.6.37. doi:10.1002/cpbi.3
• ProLIF. Bouysset C, Fiorucci S. ProLIF: a library to encode molecular interactions as fingerprints. J Cheminform. 2021;13:72. doi:10.1186/s13321-021-00548-6
• 3Dmol.js. Rego N, Koes D. 3Dmol.js: molecular visualization with WebGL. Bioinformatics. 2015;31(8):1322-1324. doi:10.1093/bioinformatics/btu829
• PyMOL. The PyMOL Molecular Graphics System, Schrodinger, LLC.

A methods paragraph you can adapt

Molecular docking was performed on ChemServer (https://chemserver.online) with AutoDock Vina 1.2. The receptor was prepared with AutoDockTools 1.5.7 (polar hydrogens and Gasteiger charges) after removing water and other hetero atoms, and the ligands were built in 3D and charged with Open Babel. The search box was centred on the co crystal ligand, and docking used an exhaustiveness of 32 with 10 binding modes. The protocol was validated by redocking the co crystal ligand, which reproduced the crystal pose with a heavy atom RMSD below 2 Å.

Change the engine, preparation method and settings to match your own run. They are all in the run's METHODS_AND_CITATIONS.txt and config.txt. For an example of a full validation, see the sample docking report.

Publications using ChemServer

Published a paper, thesis or poster that used ChemServer? Email the reference to chris@chemserver.online and we will list it here with a link to your work.