Aaron Hart

KNIME.com AG

JChem Extensions for KNIME

The KNIME Platform

KNIME Product Portfolio

KNIME Server

• All KNIME Team Space Features • Server Based • Remote Execution • Scheduled Execution • Web Portal: Workflows • Web Service • User Authentication • User Rights Management

• Automated • Web Integrated • Managed • Secure

KNIME

Team Space

• All KNIME Professional Features • Shared Workflow Repository • Shared Data Space • Shared Metanodes

• Maintainable • Shareable

KNIME

Professional

• All KNIME Features • Commercial Agreement • Professional Support • Priority Development

• Professional

• Full Function • Open Source • Extendable • 3rd Party

Integration • Scalable

• Access • Transformation • Statistics • Data Mining • Visualization • Reporting • Interactive / Batch Execution • Workflow Interface

KNIME

KN

IME

Clu

ste

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• Cluster Execution • Advanced Hardware

Utilization

KNIME Core Chemistry

• IO

• Readers and writers for Mol2, Mol, Rxn, SDF and Smiles.

• Mining

• Fingerprint Bayesian learner/predictor

• MoSS & Moss MCSS similarity

• Misc

• SDF Property extraction and Insertion

• Translators

• Molecule Type Cast converts strings to native KNIME

chemistry types

• OpenBabel translates between chemistry types

• Marvin

• Sketch, Convert and View (2d and 3d)

• Others

• Distance matrix, Similarity Search

KNIME Core Chemistry II

New Features in 2.7:

Fingerprint Bayesian Modeling

• Predict activity based on

molecular fingerprints

Similarity Search

• Find molecules similar to query

KNIME Community

Cheminformatics Contributions – RDKit

• Chemoinformatics library (supported by Novartis)

– Indigo

• Chemoinformatics library (GGA Software)

– Erlwood Chemoinformatics

• Collection of nodes geared towards pharmaceutical

research (Eli-Lilly)

– CDK

• Integration of the well-known Java library for structural

chemo-and bioinformatics (EBI)

Others In Bioinformatics, Scripting, Information Retrieval

http://www.knime.org/files/molegro_logo.png

• ChemAxon / Infocom

• Chemical Computing Group

• Schrödinger

• Cresset

• Tripos

• BioSolve IT

• Spotfire

• Molecular Discovery

• Treweren

• Korilog

• Molegro

Technology Partners – only Life Sciences –

JChem Extensions

• Extensions of ChemAxon’s tool for KNIME

workflow

• Infocom implement it with the support

of ChemAxon

• Contains over 90% of ChemAxon's

cheminformatics functionality

– Marvin Sketch

– Marvin View

– Marvin Space

– Converter

Available as part of KNIME’s core chemistry extensions

Free of charge for ALL customers!!

Marvin Family Nodes

Document to Structure

• Extracts names from text

documents (Text, PDF and HTML)

• Structure images are also

converted

• Automatic text OCR

• Also import smiles, InChI and CAS

number

• Support the common office

document formats (It’s new!)

Markush Structures

• Markush enumeration

• Markush search

• Markush structure generation

• Markush Viewer

JChem for Excel

JC4XL Reader

– Reads Excel file created with

JChem For Excel.

JC4XL Writer

– Writes JChem For Excel

compatible xlsx file.

Come to the

3rd KNIME Life Science Day

Meet the KNIME people and other customers

Hear about Life Sciences applications

Get to know community contributions

Listen to partner presentations

This Friday (28th)

at the NERD center in Cambridge, MA

Chemistry in KNIME Webinar

Sketch with Marvin

Calculate Molecular Descriptors

Read/Write Chemistry data types

Get structures from ChEMBL

www.knime.org/events (or come speak with us!)