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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. - PowerPoint PPT Presentation
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PowerMV Chemical Data Mining Environment
S. Stanley YoungJun Feng and Jack Liu
NISS
MPDM, McMaster University4 June 2005
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Outline
1. PowerMV, a chemistry data mining environment.
2. rSVD, robust singular value decomposition, Liu, Hawkins, Ghosh,Young, PNAS (2003).
3. Space-filling designs.
4. PharmID: complex problem.
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Environment
20k lines of interface code; 300k lines of algorithm code.~0.75 man-years.
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SD File, 50 years old and bad!
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 0Etc.
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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
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Viewer
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Molecule Blow Up
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3D View
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Compute Molecular Descriptors,
Drug-Like Properties
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Chemical Graphs and Properties
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Multiple Descriptor Types
Numerical Topology!
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Similarity Searching,
Motivating Paper
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Select a Target Compound
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Search Dialog
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Structure Comparison
Window
Target
Neighbor
Annotation
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Statistical Methods
17Free download : www.niss.org/PowerMV
Summary
• Display SD.
• Compute descriptors.
• Cluster.
• Statistical analysis.
• Similarity search.
Become NISS affiliate!
20k display code
300k algorithm code
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Contact Information
Stan Young [email protected] www.niss,org 919 685 9328
Jun Feng [email protected]
Become a NISS Affiliate!
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Questions / Comments ?
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Computed Properties – Rule of 5
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Structure Comparison
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Neighbor
List
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Attribute Comparison
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Annotated Data Bases
1. Stockwell ACL
2. ChemBank
3. Exploratory Centers for Chemoinformatics Research
4. Chemical Entities of Biological Interest
5. Commercial, e.g. GVK, ACS, MDDR, Ashgate
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Rule
ofFive
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Example: CNS Compounds
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Current NISS ResearchPharmID: Pharmacophore Identification
Finds multiple binding modes! Selectivity.
1. NISS research.
2. Jun Feng, CompChem.
3. Seeking collaborators.
4. Become NISS affiliate.
