Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012

Open-source softwareIndigo

Indigo KNIME nodes

Mikhail Rybalkin

Alexander Saveliev

5th KNIME Users Group Meeting and WorkshopFebruary 2, 2012

History of Indigo project

BingoOracle, Sql Server, PostgreSQL

Open-source

Mikhail RybalkinAlexander Saveliev Indigo KNIME nodes February 2, 2012



ToolsCanonical SMILES, Rendering,

Decomposition

Open-source




IndigoC, Java, Python, C#

Tools

Indigo C++ Core

Open-source





Tools

Indigo C++ Core

KnimeNodes

Open-source





Tools

Indigo C++ Core

KnimeNodes

KetcherJavascript Molecule

Sketcher

Open-source





Tools

Indigo C++ Core

KnimeNodes

KetcherJavascript Molecule

Sketcher

Proprietary projectsMass spectrometry

Molecular dynamics

Sequence processing

High-throughput screening

GPGPU, cluster computing

Image analysys and recognition

Open-source


Why Open Source?

I Bussiness model

I Relationship with the scientific commnity

I Feedback from the commnityI SuggestionsI Testing

I Experience to develop commercial projects


Why Open Source?

I Bussiness model





Why Open Source?

I Bussiness model





Indigo Nodes (Stable)


Indigo Nodes (Nightly)

IndigoCombinatorial Chemistry

Combinatorial Reaction EnumerationManipulators

AromatizerAtom Replacer

Bond Replacer

Dearomatizer

Feature RemoverHydrogen Adder

Hydrogen RemoverMolecule Nodes

Component CombinerComponent Separator

Molecule TransformationMurcko ScaffoldR-Group Decomposer

Scaffold FinderSubstructure Match CounterSubstructure Matcher

Molecule Translators

Indigo to MoleculeIndigo to Query MoleculeMolecule to IndigoQuery Molecule to Indigo

PropertiesFingerprint SimilarityIndigo FigerprintMolecule Properties

Valence Checker

Reaction NodesReaction Automapper

Reaction BuilderReaction SplitterSubstructure Matcher

Reaction Translators

Indigo to ReactionIndigo to Query ReactionReaction to IndigoQuery Reaction to Indigo


Functionallity

I Manipulators

Aromatizer Dearomatizer Hydrogen RemoverAtom Replacer Bond Replacer Feature RemoverHydrogen Adder

I Substructure search (Ordinary, Tautomer, Exact)

Parse SMILES

Parse query SMILES

Match tautomer substructure

Molecule to Indigo

Query Moleculeto Indigo

SubstructureMatcher

Parse SMILES

Parse query SMILES


Molecule to Indigo


SubstructureMatcher

O

N

Query

O

NH

Highlightedtarget molecule


Functionallity

I Manipulators

Aromatizer Dearomatizer Hydrogen RemoverAtom Replacer Bond Replacer Feature RemoverHydrogen Adder

I Substructure search (Ordinary, Tautomer, Exact)

Parse SMILES

Parse query SMILES


Molecule to Indigo


SubstructureMatcher

Parse SMILES

Parse query SMILES


Molecule to Indigo


SubstructureMatcher

O

N

Query

O

NH

Highlightedtarget molecule


Functionallity (2)

I Scaffold finder and R-Group decomposition

N

N

O

C

R1

R2

R3R4

R5

O* Cl *

O OC

C

*

O OC

C

O* Cl

O*

N

N

*

O N

CN

*

O

C

CO N*

N*'

R1 R2 R3 R4 R5

initial moleculesin SMILES

converter

scaffold detection

R-group decomposition

Table Creator Molecule to Indigo

Scaffold Finder

R-Group Decomposer

converter

scaffold detection


Table Creator

Scaffold Finder

R-Group Decomposer

I Indigo Fingerpints

Calculate fingerprints Distance matrix Cluster by Tanimoto distance

View the clusters

Indigo FingerprintDistance MatrixCalculate

Hierarchical Clustering(DistMatrix)

HierarchicalCluster ViewCalculate fingerprints Distance matrix Cluster by Tanimoto distance

View the clusters

Distance MatrixCalculate


HierarchicalCluster View


Functionallity (2)

I Scaffold finder and R-Group decomposition

N

N

O

C

R1

R2

R3R4

R5

O* Cl *

O OC

C

*

O OC

C

O* Cl

O*

N

N

*

O N

CN

*

O

C

CO N*

N*'

R1 R2 R3 R4 R5

initial moleculesin SMILES

converter

scaffold detection


Table Creator Molecule to Indigo

Scaffold Finder

R-Group Decomposer

converter

scaffold detection


Table Creator

Scaffold Finder

R-Group Decomposer

I Indigo Fingerpints

Calculate fingerprints Distance matrix Cluster by Tanimoto distance

View the clusters

Indigo FingerprintDistance MatrixCalculate


HierarchicalCluster ViewCalculate fingerprints Distance matrix Cluster by Tanimoto distance

View the clusters

Distance MatrixCalculate


HierarchicalCluster View


Whats New?

I Reaction Support

I Library Enumeration

I Molecule Transformations (Standardization)

Translator

Translator Transformation

Query Reactionto Indigo

Molecule to IndigoMoleculeTransformation

Translator




A2A1 A2A1

R1

OH

O

R1 COOH

CF31

F

1

F

F

CF3

C

O

N

O

O

OH

O

CF3

CF3

F

F F

F

F

F

COOH

O

N

O O

CF3

CF3

Source molecule Transformations Result molecule

I Builder/Splitter Nodes

I InChI, InChIKey (preliminary)

I No dependencies on other packages in RHEL, and Mac OS X


Whats New?

I Reaction Support



Translator




Translator




A2A1 A2A1

R1

OH

O

R1 COOH

CF31

F

1

F

F

CF3

C

O

N

O

O

OH

O

CF3

CF3

F

F F

F

F

F

COOH

O

N

O O

CF3

CF3






Whats New?

I Reaction Support



Translator




Translator




A2A1 A2A1

R1

OH

O

R1 COOH

CF31

F

1

F

F

CF3

C

O

N

O

O

OH

O

CF3

CF3

F

F F

F

F

F

COOH

O

N

O O

CF3

CF3






Friday Community Workshop

I Real workflow examples (by Simon)

I Indigo nodes in-depth

I Planned nodes

I Discussion

Thank you!


Friday Community Workshop

I Real workflow examples (by Simon)

I Indigo nodes in-depth

I Planned nodes

I Discussion

Thank you!


Indigo KNIME nodes · PDF fileIndigo KNIME nodes Mikhail Rybalkin Alexander Saveliev 5th KNIME Users Group Meeting and Workshop February 2, 2012

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