Cheminformatics toolkits

Cheminformatics toolkits are 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:

List of notable cheminformatics toolkits

Name License APIs Home Page Notes
CDK Open source Java http://sourceforge.net/projects/cdk/ [3][4]
ChemmineR Open source R, C++ http://manuals.bioinformatics.ucr.edu/home/chemminer [5][6]
Enalos Knime nodes Open source Knime http://tech.knime.org/community/enalos-nodes [7]
Indigo Open source C, C#, Java, Python http://lifescience.opensource.epam.com/indigo
MolEngine Proprietary .NET http://www.scilligence.com
OpenBabel Open source C, Python, Ruby http://openbabel.org/ ,[8][9]
Helium Open source C++ http://www.moldb.net/helium.html
RDKit Open source Python, C++, Java, Knime http://www.rdkit.org/
frowns Open source Python http://frowns.sourceforge.net/
OUCH Open source Haskell http://www.pharmash.com/posts/2010-08-02-ouch.html
chemf Open source Scala https://github.com/stefan-hoeck/chemf
SMSD Creative Commons Attribution Java http://www.ebi.ac.uk/thornton-srv/software/SMSD/ [10]
Accord SDK Proprietary VBA, .NET, PL/SQL http://accelrys.com/products/datasheets/accord-software-development-kit.pdf
CACTVS Proprietary, free for academia, personal use, public web services Tcl, C, C++, Python, Knime http://www.xemistry.com/academic
Daylight Proprietary C, C++, Java, Fortran http://www.daylight.com/products/toolkit.html
OpenEye Proprietary, free for academia C++, Python, C#, Java http://eyesopen.com/
Marvin, JChem Proprietary, free for academia Java, .NET, Javascript http://www.chemaxon.com
ADMET Predictor, MedChem Studio, MedChem Designer Proprietary, free for qualifying academics C++, KNIME, Pipeline Pilot http://www.simulations-plus.com

References

  1. Jean-Loup Faulon; Andreas Bender (April 2010). Handbook of Chemoinformatics Algorithms. Chapman & Hall. ISBN 1420082922.
  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 Chemical Inf. Comput. Sci. 43 (2): 493–500. doi:10.1021/ci025584y. 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. PMID 16796559.
  5. Cao, Y; Charisi, A; Cheng, LC; Jiang, T; Girke, T (2008). "ChemmineR: A Compound Mining Framework for R.". Bioinformatics 24 (15): 1733–1734. doi:10.1093/bioinformatics/btn307. PMID 18596077.
  6. Wang, Y; Backman, TW; Horan, K; Girke, T (2013). "fmcsR: Mismatch Tolerant Maximum Common Substructure Searching in R.". Bioinformatics 29 (21): 2792–4. doi:10.1093/bioinformatics/btt475. PMID 23962615.
  7. Requires Knime (http://www.knime.org/)
  8. reads and writes all chemical file formats.
  9. O’Boyle N; Banck M; James C; Morley C; Vandermeersch T; Hutchison G (2011). "Open babel: an open chemical". Journal of Cheminformatics 3 (33). doi:10.1186/1758-2946-3-33.
  10. S. Asad Rahman, Syed; M. Bashton; G. L. Holliday; R. Schrader; J. M. Thornton (2009). "Small Molecule Subgraph Detector (SMSD) Toolkit". Journal of Cheminformatics 1 (12): 12. doi:10.1186/1758-2946-1-12.
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