Download PowerMV : Molecular Viewer

PowerMV
Chemical Data Mining Environment
S. Stanley Young
Jun Feng and Jack Liu
NISS
MPDM, McMaster University
4 June 2005
1
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.
2
Environment
20k lines of interface code;
300k lines of algorithm code.
~0.75 man-years.
3
1
-ISIS20 22 0
2.0680
2.9340
2.9340
3.8000
3.8000
4.6660
4.6660
5.5321
5.5321
4.6660
3.8000
3.8000
2.9061
2.0000
2.0000
2.9061
6.4260
7.3321
7.3321
6.4260
1 2 1
2 3 1
2 4 1
4 5 1
5 6 1
Etc.
3D
0
0
0
0
0
0
0 0 0
1.5173
2.0173
3.0173
1.5173
0.5173
0.0173
-0.9827
-1.4827
-2.4827
-2.9827
-2.4827
-1.4827
-0.9480
-1.4619
-2.5035
-3.0173
-3.0173
-2.5035
-1.4619
-0.9480
0 0
0 0
0 0
0 0
0 0
0
0 0999 V2000
0.0000 C
0 0
0.0000 N
0 0
0.0000 C
0 0
0.0000 C
0 0
0.0000 C
0 0
0.0000 C
0 0
0.0000 N
0 0
0.0000 C
0 0
0.0000 C
0 0
0.0000 S
0 0
0.0000 C
0 0
0.0000 C
0 0
0.0000 C
0 0
0.0000 C
0 0
0.0000 C
0 0
0.0000 C
0 0
0.0000 C
0 0
0.0000 C
0 0
0.0000 C
0 0
0.0000 C
0 0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
SD File,
50 years old
and bad!
4
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
5
Viewer
6
Molecule Blow Up
7
3D View
8
Compute Molecular Descriptors,
Drug-Like Properties
9
Chemical Graphs and Properties
10
Multiple Descriptor Types
Numerical Topology!
11
Similarity Searching,
Motivating Paper
12
Select a Target Compound
13
Search Dialog
14
Structure
Comparison
Window
Target
Neighbor
Annotation
15
Statistical
Methods
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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
17
Contact Information
Stan Young [email protected]
www.niss,org
919 685 9328
Jun Feng
[email protected]
Become a NISS Affiliate!
18
Questions / Comments ?
19
Computed Properties – Rule of 5
20
Structure Comparison
21
Neighbor
List
22
Attribute Comparison
23
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
of
Five
25
Example: CNS Compounds
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Current NISS Research
PharmID: Pharmacophore Identification
1. NISS research.
2. Jun Feng, CompChem.
3. Seeking collaborators.
4. Become NISS affiliate.
Finds multiple binding modes! Selectivity.
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