Citation

Please follow the guidelines in this document to cite use of our products in research publications and other documents.

For more information, please contact OpenEye Support.

Orion^®

To cite use of Orion, please use the following:

Orion <version-number>. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.

For example:

Orion 2025.1. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.

The version number for Orion appears in the product’s release notes, for example, https://docs.eyesopen.com/orion-user-interface/releasenotes/index.html.

Orion Floes

To cite use of an Orion-based floe package, please use the following:

OpenEye <package-name> <version-number>. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.

For example:

OpenEye Large-Scale Floes 4.2.3. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.

The version number for a floe package is displayed on the first page of the package’s release notes. For example: https://docs.eyesopen.com/floe/modules/large_scale_floes/docs/source/releasenotes_2025_1.html.

Toolkits and Applications

To cite OpenEye toolkits or applications used in your work, please use the following:

OpenEye Toolkits [or Applications] <version-number>. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.

For example:

OpenEye Toolkits 2024.2.1. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.

The Applications and Toolkits are released as a package, multiple times per year. The first part of the version number designates the calendar year. The version number appears on the summary document for the package.

If you want to cite an individual application or toolkit, you can use the syntax:

<product name> <version-number>. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.

where <product name> is:

• Bioisostere TK

• OEChem TK

• OEDepict TK

• OEDocking TK

• OEFF TK

• Eon TK

• FastROCS TK

• Grapheme TK

• GraphSim TK

• Lexichem TK

• OEMedChem TK

• MolProp TK

• Omega TK

• Quacpac TK

• Shape TK

• Spicoli TK

• Spruce TK

• Szmap TK

• Szybki TK

• Zap TK

• AFITT Application

• BROOD Application

• OEDocking Application

• EON Application

• OMEGA Application

• PICTO Application

• pKa-Prospector Application

• QUACPAC Application

• ROCS Application

• SiteHopper Application

• SPRUCE Application

• SZMAP Application

• SZYBKI Application

• VIDA Application

You can use the version number of the individual Application or Toolkit. For example:

SZYBKI Application 2.8.0.1. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.

Szybki TK 2.8.0.1. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.

The first documentation pages give the product names and version numbers, as in https://docs.eyesopen.com/applications/szybki/index.html and https://docs.eyesopen.com/toolkits/python/szybkitk/index.html.

Publications for Bibliographies

Please also cite these publications if the corresponding product was used in your research.

Orion

Sørensen, J., Bannan, C.C., Calabrò, G., Jain, V., Ovanesyan, G., Smith, A., Zhang, S., Bayly, C.I., Darden, T.A., Geballe, M.T., LeBard, D.N., McGann, M., Moon, J.B., Muddana, H.S., Shewmaker, A., LaFon, J., Tolbert, R.W., Skillman, A.G., Nicholls, A. Orion® A Cloud-Native Molecular Design Platform. In Computational Drug Discovery. V. Poongavanam and V. Ramaswamy, Eds. Wiley-VCH, 2024; pp. 579–615. DOI: 10.1002/9783527840748.ch24

AFITT and FLYNN Applications

Wlodek, S.; Skillman, A.G.; Nicholls, A. Automated Ligand Placement and Refinement with a Combined Force Field and Shape Potential. Acta Crystallogr., Sect. D: Struct. Biol. 2006, 62 (7), 741–749. DOI: 10.1107/s0907444906016076

OEDocking Application and Toolkit

Kelley, B.P.; Brown, S.P.; Warren, G.L.; Muchmore, S.W. POSIT: Flexible Shape-Guided Docking For Pose Prediction. J. Chem. Inf. Model. 2015, 55 (8), 1771-1780. DOI: 10.1021/acs.jcim.5b00142

McGann, M. FRED Pose Prediction and Virtual Screening Accuracy. J. Chem. Inf. Model. 2011, 51 (3), 578-596. DOI: 10.1021/ci100436p

McGann, M. FRED and HYBRID Docking Performance on Standardized Datasets. J. Comput.-Aided Mol. Des. 2012, 26 (8), 897-906. DOI: 10.1007/s10822-012-9584-8

OMEGA Application and Toolkit

If you are using OMEGA in torsion driving mode, please cite the following two publications.

Hawkins, P.C.D.; Skillman, A.G.; Warren, G.L.; Ellingson, B.A.; Stahl, M.T. Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and the Cambridge Structural Database. J. Chem. Inf. Model. 2010, 50 (4), 572-584. DOI: 10.1021/ci100031x

Hawkins, P.C.D. and Nicholls, A. Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures. J. Chem. Inf. Model. 2012, 52 (11), 2919–2936. DOI: /10.1021/ci300314k

If you are using OMEGA in macrocyle mode, please cite the following.

Hawkins, P.C.D. and Wlodek, S. Decisions with Confidence: Application to the Conformation Sampling of Molecules in the Solid State. J. Chem. Inf. Model. 2020, 60 (7), 3518–3533. DOI: /10.1021/acs.jcim.0c00358

ROCS Application

Hawkins, P.C.D.; Skillman, A.G.; Nicholls, A. Comparison of Shape-Matching and Docking as Virtual Screening Tools. J. Med. Chem. 2007, 50 (1), 74-82. DOI: 10.1021/jm0603365

OpenEye MMDS Web Service

To cite use of the Macromolecular Data Service (MMDS) web service, please use the syntax:

Macromolecular Data Service <version-number>. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.

For example:

Macromolecular Data Service 1.1. OpenEye, Cadence Molecular Sciences, Santa Fe, NM. http://www.eyesopen.com.

The MMDS version number appears on the web service’s release notes.