Open Babel

Open Babel
Developer(s)	Open Babel development team
Initial release	2 June 2005; 19 years ago
Stable release	3.1.1 / 8 May 2020; 4 years ago
Repository	www.github.com/openbabel/openbabel
Written in	C, C++ (wxWidgets)
Operating system	Windows, macOS, Linux, Android
Platform	IA-32, x86-64
Available in	English
Type	Cheminformatics, molecular modelling
License	GPL 2.0
Website	www.openbabel.org

Open Babel is a free chemical informatics software designed to facilitate the conversion of Chemical file formats and manage molecular data.^[3] It serves as a chemical expert system, widely used in fields such as cheminformatics, molecular modelling, and computational chemistry. Open Babel provides both a comprehensive library and command-line utilities, making it a versatile tool for researchers, developers, and professionals.^[4]

About

Due to the strong relationship to informatics this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix, Linux, macOS, and Android. It is free and open-source software released under a GNU General Public License (GPL) 2.0.

The project's stated goal is: "Open Babel is a community-driven scientific project assisting both users and developers as a cross-platform program and library designed to support molecular modeling, chemistry, and many related areas, including interconversion of file formats and data."

History

Open Babel and JOELib were derived from the OELib cheminformatics library. In turn, OELib was based on ideas in the original chemistry program Babel and an unreleased object-oriented programming library called OBabel.

Major features

chemical expert system
interconversion of many chemical file formats
substructure search, based on simplified molecular-input line-entry system (SMILES)
fingerprint calculation
3D coordinate generation^[5]
wrappers for Python, Perl, Java, Ruby, C#^[6]

Applications

In cheminformatics, Open Babel facilitates the management of molecular data through substructure searching and molecular fingerprint calculations. These functionalities enable similarity analysis, dataset clustering, and efficient organization of chemical libraries, making it suitable for large-scale workflows.

In drug discovery, Open Babel supports tasks such as preparing chemical libraries for high-throughput virtual screening and standardizing molecular formats for structure-based drug design. The software's ability to generate 3D molecular coordinates and calculate molecular descriptors is particularly valuable in predicting properties such as solubility, reactivity, and toxicity.^[7]

References

^ "Release 3.1.1". 8 May 2020. Retrieved 9 May 2020.
^ "Debian -- Details of package openbabel-gui in jessie". Retrieved 2017-03-10.
^ O'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. (2011). "Open Babel: An open chemical toolbox". Journal of Cheminformatics. 3: 33. doi:10.1186/1758-2946-3-33. PMC 3198950. PMID 21982300.
^ "Frequently Asked Questions — Open Babel openbabel-3-1-1 documentation". openbabel.org. Retrieved 2024-11-28.
^ Yoshikawa, Naruki; Hutchison, Geoffrey R. (1 August 2019). "Fast, efficient fragment-based coordinate generation for Open Babel". Journal of Cheminformatics. 11 (1): 49. doi:10.1186/s13321-019-0372-5. PMC 6676618. PMID 31372768.
^ "Open Babel - the chemistry toolbox — Open Babel openbabel-3-1-1 documentation". openbabel.org. Retrieved 2024-02-18.
^ "Bringing Open Source to Drug Discovery" (PDF). rsc.org. Retrieved 2024-11-28.
^ Guha, R.; Howard, M. T.; Hutchison, G. R.; Murray-Rust, P.; Rzepa, H.; Steinbeck, C.; Wegner, J.; Willighagen, E. L. (2006). "The Blue Obelisk - Interoperability in Chemical Informatics". Journal of Chemical Information and Modeling. 46 (3): 991–998. doi:10.1021/ci050400b. PMC 4878861. PMID 16711717.

External links

Official website
E-BABEL – interactive version of the Open Babel at Virtual Computational Chemistry Laboratory
chemCast Episode 003 – project lead developer Geoff Hutchison was interviewed on the podcast

[wikidata-8f299f9af733cfdda6853dee67bd60072cafbf5d-v18-1] "Release 3.1.1". 8 May 2020. Retrieved 9 May 2020.

[2] "Debian -- Details of package openbabel-gui in jessie". Retrieved 2017-03-10.

[OBoyle2011-3] O'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. (2011). "Open Babel: An open chemical toolbox". Journal of Cheminformatics. 3: 33. doi:10.1186/1758-2946-3-33. PMC 3198950. PMID 21982300.

[4] "Frequently Asked Questions — Open Babel openbabel-3-1-1 documentation". openbabel.org. Retrieved 2024-11-28.

[5] Yoshikawa, Naruki; Hutchison, Geoffrey R. (1 August 2019). "Fast, efficient fragment-based coordinate generation for Open Babel". Journal of Cheminformatics. 11 (1): 49. doi:10.1186/s13321-019-0372-5. PMC 6676618. PMID 31372768.

[6] "Open Babel - the chemistry toolbox — Open Babel openbabel-3-1-1 documentation". openbabel.org. Retrieved 2024-02-18.

[7] "Bringing Open Source to Drug Discovery" (PDF). rsc.org. Retrieved 2024-11-28.

[8] Guha, R.; Howard, M. T.; Hutchison, G. R.; Murray-Rust, P.; Rzepa, H.; Steinbeck, C.; Wegner, J.; Willighagen, E. L. (2006). "The Blue Obelisk - Interoperability in Chemical Informatics". Journal of Chemical Information and Modeling. 46 (3): 991–998. doi:10.1021/ci050400b. PMC 4878861. PMID 16711717.

[1]