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PowerMV Chemical Data Mining Environment

PowerMV Chemical Data Mining Environment. S. Stanley Young Jun Feng and Jack Liu NISS MPDM, McMaster University 4 June 2005. Outline. PowerMV, a chemistry data mining environment. rSVD, robust singular value decomposition, Liu, Hawkins, Ghosh,Young, PNAS (2003). Space-filling designs.

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PowerMV Chemical Data Mining Environment

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  1. PowerMV Chemical Data Mining Environment S. Stanley Young Jun Feng and Jack Liu NISS MPDM, McMaster University 4 June 2005

  2. Outline • PowerMV, a chemistry data mining environment. • rSVD, robust singular value decomposition, Liu, Hawkins, Ghosh,Young, PNAS (2003). • Space-filling designs. • PharmID: complex problem.

  3. Environment 20k lines of interface code; 300k lines of algorithm code. ~0.75 man-years.

  4. 1 -ISIS- 3D 20 22 0 0 0 0 0 0 0 0999 V2000 2.0680 1.5173 0.0000 C 0 0 0 0 0 2.9340 2.0173 0.0000 N 0 0 0 0 0 2.9340 3.0173 0.0000 C 0 0 0 0 0 3.8000 1.5173 0.0000 C 0 0 0 0 0 3.8000 0.5173 0.0000 C 0 0 0 0 0 4.6660 0.0173 0.0000 C 0 0 0 0 0 4.6660 -0.9827 0.0000 N 0 0 0 0 0 5.5321 -1.4827 0.0000 C 0 0 0 0 0 5.5321 -2.4827 0.0000 C 0 0 0 0 0 4.6660 -2.9827 0.0000 S 0 0 0 0 0 3.8000 -2.4827 0.0000 C 0 0 0 0 0 3.8000 -1.4827 0.0000 C 0 0 0 0 0 2.9061 -0.9480 0.0000 C 0 0 0 0 0 2.0000 -1.4619 0.0000 C 0 0 0 0 0 2.0000 -2.5035 0.0000 C 0 0 0 0 0 2.9061 -3.0173 0.0000 C 0 0 0 0 0 6.4260 -3.0173 0.0000 C 0 0 0 0 0 7.3321 -2.5035 0.0000 C 0 0 0 0 0 7.3321 -1.4619 0.0000 C 0 0 0 0 0 6.4260 -0.9480 0.0000 C 0 0 0 0 0 1 2 1 0 0 0 2 3 1 0 0 0 2 4 1 0 0 0 4 5 1 0 0 0 5 6 1 0 0 0 Etc. SD File, 50 years old and bad!

  5. Smiles Chemical Notation CC1=CC=C(C=C1)S(=O)(=O)N(CC(O)=O)C2=CC(Cl)=CC=C2 CC1CCC(CC1)C(C)(C)C(CC(C)C)C2CCCC(C)C2

  6. Viewer

  7. Molecule Blow Up

  8. 3D View

  9. Compute Molecular Descriptors,Drug-Like Properties

  10. Chemical Graphs and Properties

  11. Multiple Descriptor Types Numerical Topology!

  12. Similarity Searching,Motivating Paper

  13. Select a Target Compound

  14. Search Dialog

  15. Structure Comparison Window Target Neighbor Annotation

  16. Statistical Methods

  17. Summary • Display SD. • Compute descriptors. • Cluster. • Statistical analysis. • Similarity search. • Become NISS affiliate! • 20k display code • 300k algorithm code Free download : www.niss.org/PowerMV

  18. Contact Information Stan Young young@niss.org www.niss,org 919 685 9328 Jun Feng feng@niss.org Become a NISS Affiliate!

  19. Questions / Comments ?

  20. Computed Properties – Rule of 5

  21. Structure Comparison

  22. Neighbor List

  23. Attribute Comparison

  24. Annotated Data Bases • Stockwell ACL • ChemBank • Exploratory Centers for Chemoinformatics Research • Chemical Entities of Biological Interest • Commercial, e.g. GVK, ACS, MDDR, Ashgate

  25. RuleofFive

  26. Example: CNS Compounds

  27. Current NISS ResearchPharmID: Pharmacophore Identification • NISS research. • Jun Feng, CompChem. • Seeking collaborators. • Become NISS affiliate. Finds multiple binding modes! Selectivity.

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