evotec - knime desktop tools for chemists

Building innovative

drug discovery alliances

Knime – Desktop tools for chemists

Evotec AG, Knime – desktop tools for chemists, May 2011

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Agenda

1

Knime

Getting project data from Excel spreadsheets

Getting project data from IJC databases

Getting public data from databases

Enumerating libraries of compounds

Getting data from other databases

Knime Server

Knime node development

Conclusions

A KNIME Solution

The Multi-Purpose Tool in the MedChem Toolkit

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KNIME

The Multi-Purpose Tool in the MedChem Toolkit

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Knime Workbench

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Agenda

5

Knime






Knime Server


Conclusions

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Extracting data from Excel

Loading into IJC

Project compound data is kept on an Excel spreadsheet

Data is filtered and prepared for loading into an IJC database

Additional calculations are carried out during the workflow

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Agenda

7

Knime






Knime Server


Conclusions

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Using InstantJChem databases

Projects keep their data in Oracle

Every project uses InstantJChem for their project data Project members can easily view and query their data

Easy for project members to load new data and maintain old data

Two schemas; one for project data, one for project ideas

Additional properties can be calculated during data loading

Shared Oracle database All data backed up

Each project area is secure

Only project members can see the data

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Overview

9

Shared IJC project database setup at Evotec

Enterprise licenses for server use shared across Abingdon and Hamburg sites

Dedicated IJC server at Abingdon with Oracle 10g and JChem cartridge

One Oracle schema per drug discovery project containing project data (currently 40 live IJC

shared projects)

A project IJC schema is connected to each Oracle schema

Built-in IJC security & roles used for user management

Deployment to project users via web server URLs

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Project Data Flow

Drug Discovery IJC Project at Evotec

Compound

Registration

Medicinal

Chemistry

ADMET

10g

IJC 5.3.1

JChem 5.3.1

Abingdon

Opera™

Assays

Counter

Assays

In Vivo

Hamburg

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Extract data from IJC

Project ideas database

Project chemists add synthetic ideas to their IJC database

Knime is used to extract the data that has been added that month

The extracted data is presented in PowerPoint

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Data Model

Schema Editor view: Data Trees

SAR data tree contains joined chemistry &

biology tables, allowing many assay results for

each assay type per compound structure

Assay

tables

Structure table fields

Relationships

All Structures

Bioassay ADMET assays

1-n1-n

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Creating SAR tables from databases

Producing reports

Project data can be queried and filtered

easily

Data from multiple tables can be used

Additional properties can be calculated

SAR table reports can be prepared

from the filtered data

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Extracting data from IJC

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Using activity data

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Exporting data from multiple tables

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Easy data extraction from IJC

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Agenda

16

Knime

Getting project data from Excel





Knime Server


Conclusions

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Accessing public data

Viewing ChEMBL data

ChEMBL is a database of

bioactive drug-like small

molecules, it contains 2-D

structures, calculated properties

(e.g. logP, Molecular Weight,

Lipinski Parameters, etc.) and

abstracted bioactivities (e.g.

binding constants, pharmacology

and ADMET data

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Accessing public data

Viewing ChEMBL data through IJC

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Searching the ChemBL database

Easy access to ChEMBl data using Knime

A simple workflow allows users to search the ChEMBl data

Users don’t need a username and password

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Agenda

20

Knime

Getting data from Excel spreadsheets




Knime Server


Conclusions

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Library enumeration

An easy way for chemists to create compounds

Chemists can quickly create a virtual library

Calculate physical properties

Select interesting compounds for further processing

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Virtual Library Enumeration: CDK2 Example

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Re-usable components

Physical properties

Parts of workflows can be re-used

Often used operations can be bundled into meta nodes

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Even more meta nodes!

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Library enumeration and searching

Check EVOsource for starting materials

Enumerate a focused library

Select the promising

compounds

Search in-house compound

database for starting

materials

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Agenda

26

Knime

Getting data from Excel spreadsheets





Knime Server / Sharing Workflows


Conclusions

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Search Compound database

Retrieving hits from EVOsource

Using a list of part ID’s

Get lists of suppliers that the compound can be bought from

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Administration of the ELN

Auditing users

Connect to ELN database

Carry out audits By project

By user

Regular

Leavers

Submitted, countersigned, Printed

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Agenda

29

Knime



Getting data from public data sets





Conclusions

PAGE

Knime Server

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Sharing workflows

Workflows created by expert users

Reports for other users

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SharePoint

31

Sharing workflows

Using SharePoint to share workflows and tips

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Agenda

32

Knime






Knime server / Sharing Workflows


Conclusions

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EVOnodes

KNIME Development Projects

Have developed KNIME nodes to run linux based CADD programs

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EVOnodes

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Knime development projects

Knime nodes to replace

Evotec desktop modelling

tool

Allow integrating modelling

tools in workflows

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Agenda

35

Knime








Conclusions

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Conclusions

36

Why use Knime?

On every chemists desktop

Easy for chemists to tailor make database exports

Easy for chemists to enumerate libraries

Easy for chemists to generate tailor made reports from databases

Simple for developers and computational chemists to extend

Fun to work with!

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Acknowledgements

37

eScience Ian Berry

Catherine Reisser

Mike Potterton

Computational Chemistry Mike Mazanetz

Michelle Szeto

Discovery Chemistry Ed Walker

Rich Jones

Chris Stimson

Your contact:

Building innovative

drug discovery alliances

Dr Bob MarmonSenior Applications Developer, eScience

+44.(0).1235.861561 +44.(0)[email protected]

evotec - knime desktop tools for chemists

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