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:

  • 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
NameLicenseAPIsHome PageNotes
CDKOpen sourceJavahttp://sourceforge.net/projects/cdk/[3][4]
ChemmineROpen sourceR, C++http://manuals.bioinformatics.ucr.edu/home/chemminer[5][6]
Enalos KNIME nodesOpen sourceKNIMEhttp://tech.knime.org/community/enalos-nodes[7]
Enalos+ KNIME nodesProprietaryKNIMEhttp://enalosplus.novamechanics.com/[8]
IndigoOpen sourceC, C#, Java, Pythonhttp://lifescience.opensource.epam.com/indigo
MolEngineProprietary.NEThttp://www.scilligence.com
Molecular Operating Environment (MOE)ProprietaryScientific Vector Languagehttps://web.archive.org/web/20160909172415/http://www.chemcomp.com/MOE-Cheminformatics_and_QSAR.htm
OpenBabelOpen sourceC, Python, Rubyhttp://openbabel.org/,[9][10]
HeliumOpen sourceC++https://web.archive.org/web/20140407082845/http://www.moldb.net/helium.html
RDKitOpen sourcePython, C++, Java, Knimehttp://www.rdkit.org/
RcpiOpen sourceRhttps://bioconductor.org/packages/Rcpi[11]
frownsOpen sourcePythonhttp://frowns.sourceforge.net/
OUCHOpen sourceHaskellhttp://www.pharmash.com/posts/2010-08-02-ouch.html
chemfOpen sourceScalahttps://github.com/stefan-hoeck/chemf
3D-e-ChemOpen sourcePython, Java, Knimehttps://3d-e-chem.github.io/[12][13]
SMSDCreative Commons AttributionJavahttp://www.ebi.ac.uk/thornton-srv/software/SMSD/[14]
Accord SDKProprietaryVBA, .NET, PL/SQLhttp://accelrys.com/products/datasheets/accord-software-development-kit.pdf
CACTVSProprietary, free for academia, personal use, public web servicesTcl, C, C++, Python, Knimehttp://www.xemistry.com/academic
DaylightProprietaryC, C++, Java, Fortranhttp://www.daylight.com/products/toolkit.html
OEChemProprietary, free for academiaC++, Python, C#, Javahttp://eyesopen.com/
Marvin, JChemProprietary, free for academiaJava, .NET, Javascripthttp://www.chemaxon.com
ChemDoodle APIProprietaryJava, Javascripthttp://www.ichemlabs.com
PerlMolOpen sourcePerlhttps://web.archive.org/web/20120315121757/http://www.perlmol.org/
ADMET Predictor, MedChem Studio, MedChem DesignerProprietary, free for qualifying academicsC++, KNIME, Pipeline Pilothttp://www.simulations-plus.com
CDD Vault Proprietary, free for CDD Public read-only data CDD Vault https://www.collaborativedrug.com/cdd-vault [15]
MolecularGraph.jl MIT License Julia https://github.com/mojaie/MolecularGraph.jl
gollark: <@201096871341588480> That's not the IP the requests are being sent from. I assume the quotas are actually being *tracked* somewhere, and *that quota is probably wrong* if you're getting the random bits via HTTP request from your proxy.
gollark: But *why*?
gollark: IPv6 is becoming increasingly important, what with all the issues with IPv4 address availability.
gollark: Also, your way would probably cause IPv6 issues, but I assume you don't care about that either.
gollark: Assuming you actually want to use the random.org API and not just get the quota of your IP for no reason, random.org will see all the requests as coming from the proxy, because they *are*, and reduce your quota based on that, *not* the IP of your CC computer.

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 Chemical 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. 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. PMC 2638865. 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. Requires KNIME (http://www.knime.org/)
  9. reads and writes all chemical file formats.
  10. 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.
  11. Cao DS, Xiao N, Xu QS, Chen AF (Jan 2015). "Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions". Bioinformatics. 31 (2): 279–281. doi:10.1093/bioinformatics/btu624. PMID 25246429.
  12. McGuire R, Verhoeven S, Vass M, Vriend G, de Esch IJ, Lusher SJ, Leurs R, Ridder L, Kooistra AJ, Ritschel T, de Graaf C (2017). "3D-e-Chem-VM: Structural cheminformatics research infrastructure in a freely available Virtual Machine". J. Chem. Inf. Model. 57 (2): 115–121. doi:10.1021/acs.jcim.6b00686. PMC 5342320. PMID 28125221.
  13. Kooistra AJ, Vass M, McGuire R, Leurs R, de Esch IJ, Vriend G, Verhoeven S, de Graaf C (2018). "3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery". ChemMedChem. 13 (6): 614–626. doi:10.1002/cmdc.201700754. PMC 5900740. PMID 29337438.
  14. 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. PMC 2820491. PMID 20298518.
  15. Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery. Hohman M, Gregory K, Chibale K, Smith PJ, Ekins S, Bunin B Drug Discov Today. 2009 Mar;14(5-6):261-70.
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