Molecule mining

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This page describes mining for molecules. Since molecules are multi-labeled graphs this is strongly related to graph mining and structured data mining. The main problem is how to represent molecules while discriminating the data instances. One way to do this is chemical similarity metrics, which has a long tradition in the field of cheminformatics.

Typical approaches to calculate chemical similarities use chemical fingerprints, but this loses the underlying information about the molecule topology. Mining the molecular graphs directly avoids this problem. So does the inverse QSAR problem which is preferable for vectorial mappings.

Coding(Molecule_i,Molecule_ji)

Kernel methods

• Marginalized graph kernel^[1]

• Optimal assignment kernel^[1][1][1]

• Pharmacophore kernel^[1]

Maximum Common Graph methods

• MCS-HSCS^[1] (Highest Scoring Common Substructure (HSCS) ranking strategy for single MCS)

Coding(Molecule_i)

Molecular query methods

• MoFa/MoSS^[1][1][1]
• ParMol^[1] (contains MoFa, FFSM, gSpan, and Gaston)
• PolyFARM^[1]
• SMIREP^[1]
• Warmr^[1][1]
• AGM^[1][1]
• DMax^[1]
• Gaston^[1]
• optimized gSpan^[1][1]
• MolFea^[1]
• SAm/AIm/RHC^[1]
• LAZAR^[1]

See also

• Molecular Query Language

References

• Schölkopf, B., K. Tsuda and J. P. Vert: Kernel Methods in Computational Biology, MIT Press, Cambridge, MA, 2004.
• R.O. Duda, P.E. Hart, D.G. Stork, Pattern Classification, John Wiley & Sons, 2001. ISBN 0-471-05669-3
• Gusfield, D., Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology, Cambridge University Press, 1997. ISBN 0-521-58519-8
• R. Todeschini, V. Consonni, Handbook of Molecular Descriptors, Wiley-VCH, 2000. ISBN 3527299130

See also

• QSAR
• ADME
• partition coefficient

External links

• 5th International Workshop on Mining and Learning with Graphs, 2007
• Overview for 2006
• Molecule mining (basic chemical expert systems)
• ParMol and master thesis documentation - Java - Open source - Distributed mining - Benchmark algorithm library
• TU München - Kramer group
• Molecule mining (advanced chemical expert systems)
• DMax Chemistry Assistant - commercial software

Acknowledgement and Attribution Regarding Sources of Content

Some of the initial content on this page may be incorporated in part from copyleft sources in the public domain including wikis such as Wikipedia and AskDrWiki. Drug information for patients came from the The National Library of Medicine. Infectious disease information may have come from the Centers for Disease Control (CDC). Differential Diagnoses are drawn from clinicians as well as an amalgamation of 3 sources: 1.The Disease Database; 2. Kahan, Scott, Smith, Ellen G. In A Page: Signs and Symptoms. Malden, Massachusetts: Blackwell Publishing, 2004:3; 3. Sailer, Christian, Wasner, Susanne. Differential Diagnosis Pocket. Hermosa Beach, CA: Borm Bruckmeir Publishing LLC, 2002:7 .