List of cheminformatics toolkits

Cheminformatics toolkits are notable software development kits that allow cheminformaticians to develop custom computer applications for use in virtual screening, chemical database mining, and structure-activity studies.^[1][2] Toolkits are often used for experimentation with new methodologies. Their most important functions deal with the manipulation of chemical structures and comparisons between structures. Programmatic access is provided to properties of individual bonds and atoms.

Functionality

Toolkits provide the following functionality:

• Read and save structures in various chemistry file formats.
• Determine if one structure is a substructure of another (substructure matching).
• Determine if two structures are equal (exact matching).
• Identification of substructures common to structures in a set (maximal common substructure, MCS).
• Disassemble molecules, splitting into fragments.
• Assemble molecules from elements or submolecules.
• Apply reactions on input reactant structures, resulting in output of reaction product structures.
• Generate molecular fingerprints. Fingerprints are bit-vectors where individual bits correspond to the presence or absence of structural features. The most important use of fingerprints is in indexing of chemistry databases.

List of notable cheminformatics toolkits

Name	License	APIs	Home Page	Notes
CDK	Open source	Java, R, Python	https://cdk.github.io/	[3][4][5]
Indigo	Open source	Java, .NET, Python	https://github.com/epam/Indigo
Molecular Operating Environment (MOE)	Proprietary	Scientific Vector Language	https://web.archive.org/web/20160909172415/http://www.chemcomp.com/MOE-Cheminformatics_and_QSAR.htm
Open Babel	Open source	C++, Python, Java, Perl, C#, Ruby	http://openbabel.org/	,[6][7]
RDKit	BSD-3-Clause License	C++, Python	https://www.rdkit.org/

References

1. Jean-Loup Faulon; Andreas Bender (April 2010). Handbook of Chemoinformatics Algorithms. Chapman & Hall. ISBN 978-1420082920.
2. Johann Gasteiger (November 2003). Chemoinformatics. Wiley-VCH. ISBN 3527306811.
3. Steinbeck C, C.; Han Y; Kuhn S; Horlacher O; Luttmann E; Willighagen E (2003). "The Chemistry Development Kit". J. Chem. Inf. Comput. Sci. 43 (2): 493–500. doi:10.1021/ci025584y. PMC 4901983. PMID 12653513.
4. Steinbeck C., Christoph; Hoppe C.; Kuhn S.; Floris M.; Guha R.; Willighagen E.L. (2006). "Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics". Curr. Pharm. Des. 12 (17): 2111–2120. doi:10.2174/138161206777585274. hdl:2066/35445. PMID 16796559.
5. Willighagen, Egon L.; Mayfield, John W.; Alvarsson, Jonathan; Berg, Arvid; Carlsson, Lars; Jeliazkova, Nina; Kuhn, Stefan; Pluskal, Tomáš; Rojas-Chertó, Miquel; Spjuth, Ola; Torrance, Gilleain; Evelo, Chris T.; Guha, Rajarshi; Steinbeck, Christoph (December 2017). "The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching". Journal of Cheminformatics. 9 (1): 33. doi:10.1186/s13321-017-0220-4. PMC 5461230. PMID 29086040. S2CID 2019985.
6. reads and writes all chemical file formats.
7. O’Boyle N; Banck M; James C; Morley C; Vandermeersch T; Hutchison G (2011). "Open babel: an open chemical". Journal of Cheminformatics. 3 (33): 33. doi:10.1186/1758-2946-3-33. PMC 3198950. PMID 21982300.