BIOMOLECULES IN R&D INFORMATICS - ChemAxon...More on this by Jarrod Medeiros, IDBS IDBS EWB Web...

BIOMOLECULES IN

R&D INFORMATICS

Roland Knispel

Cyclosporin A

Draw or useName to Structure:Ciclosporin

In default monomer set Not in default monomer set

AALLVTAGLVL

Sequence

Chemical structure

Co

nve

rsio

n

BIOEDDIE

A JS-based HELM editor for the web

Eddie

- JS application for all

major browsers

- Easy editing

- No-structure

components

- Native support for

MOL/HELM/sequence

BioEddie

BioEddie


major browsers

- Easy editing

- No-structure

components


MOL/HELM/sequence

- Customizable views

- Multi-level annotations


major browsers

- Easy editing

- No-structure

components


MOL/HELM/sequence

- Customizable views

- Multi-level annotations

- NEW: sequence

domain support (Abs)

BioEddie

BioEddie: Oxytocin from sequence or MOL file

• API (Java and REST-ful) for

– Native HELM support (HELM, HELM2, xHELM)

– Standardization

– Centralized DB storage

– Registration of entities and batches with custom business

logic

– Search by sequence/chemical structure/metadata

– Conversion to/from Mol/FASTA/HELM

– Property calculations

• Integrates with

– Since v16.8.1: Instant JChem, planned: Plexus Connect

– Texelia BioScity, planned: IDBS E-WorkBook

Biomolecule Toolkit

CASE STUDY: CHEMBL V21

Tools for getting started with HELM, and content curation

• 19773 peptide

biotherapeutics with

associated activity data

• Molecules served as HELM

or chemical structure file

• ChEMBL interface:

searchable by CompoundID,

chemical structure or select

metadata

CHEMBL v21

- KNIME

- Standardizer node

Ungroup S-groups, Strip

salts/solvents, Remove

explicit hydrogens,

Neutralize structure,

Aromatize, Standardize

functional groups

Standardize Convert Canonicalize Store/Search

CHEMBL297610

Tools used

- KNIME

- Biomolecule Toolkit

- BioEddie for image

rendering

- 3 wrong

conversions in

ChEMBL data set

identified


PEPTIDE1{E.C.G.[X1091]}$$$$

wrong

PEPTIDE1{E}|PEPTIDE2{C.G.[X10

91]}$PEPTIDE1,PEPTIDE2,1:R3-

1:R1$$$

correct

Tools used

CHEMBL223118

- KNIME


- 864 HELM

notations in

ChEMBL changed

- Allows direct

comparison of

HELM notations


Tools used

Before:

PEPTIDE1{[ac].[dE].[Phe(4-Cl)].[d3-

Pal]}|PEPTIDE2{D.R.[dNal].L.K}|PEPT

IDE3{P.[dDpr].[am]}$PEPTIDE2,PEPT

IDE3,5:R2-

1:R1|PEPTIDE2,PEPTIDE1,5:R3-



1:R3$$$Before:

PEPTIDE1{G.Y.G.F}$PEPTIDE1,PEPTID

E1,4:R2-1:R1$$$

After:

PEPTIDE1{F.G.Y.G}$PEPTIDE1,PEPTID

E1,4:R2-1:R1$$$

After:

PEPTIDE1{[ac].[dE].[Phe(4-Cl)].[d3-

Pal].D.R.[dNal].L.K.P.[dDpr].[am]}$PEPTI

DE1,PEPTIDE1,11:R3-


2:R3$$$

CHEMBL412009

CHEMBL42623


Search by:

- Sequence (incl.

wildcards)

- Chemical structure

- Modifications

- Metadata


Tools used

Query # hits

Molecules containing „Oxytocin“ in name

field2

Molecules with the natural analogue

sequence of Oxytocin18

Oxytocin-like sequences with non-standard

amino acids17

Oxytocin derivatives containing the

chemical structure of penicillamine3

Oxytocin derivatives containing the L-

penicillamine monomer2

USE CASE: ANTIBODY REGISTRATION

Using Instant JChem/MiniReg + Biomolecule Toolkit

Customer specification of an antibody:

• VL sequence / sequence (EIVLWQSPGT…)

• VH sequence / sequence (QVQIVQSGAE…)

• Fv backbone (scaffold) / text field (“CBr6”)

- Antibody definitions registered from file template

- Duplicate check and batch handling

- Assay data uploading

- Form views and reporting

Antibody registration

Delivered to the customer

BIOMOLECULE TOOLKIT AS A

PLATFORM

Registration DB

Architecture

Biomolecule Toolkit

Java API

REST-ful WS

Files (e.g. MOL,

FASTA, HELM)

Registration Client

Web

JChem for Office

Plexus Connect

Instant JChemSince 16.8.1

Q4

Your application

- Create new project

pointing to

Biomolecule Toolkit

DB

- Grid view with

molecule visualization

Since v16.8.1: Biomolecules in Instant JChem

- Create new project

pointing to

Biomolecule Toolkit

DB

- Grid view with

molecule visualization

- Form views with

additional data

- Querying

Since v16.8.1: Biomolecules in Instant JChem

Texelia BioScity - Data management/tracking and inventory for the Bio/Chem lab

BioScity

More on this by Jarrod Medeiros, IDBS

IDBS EWB Web – bringing HELM support into an ELN

Mockups only!!! – POC development won‘t be possible til UGM

HELM (auto-generated): untitled_molecule_file3.mol

HELM (auto-generated):

untitled_mole...

Proof of concept – to be delivered to customers 2017

IDBS EWB Web – bringing HELM support into an ELN

Mockups only!!! – POC development won‘t be possible til UGM

HELM (auto-generated): untitled_molecule_file3.mol

HELM (auto-generated):

untitled_mole...

ROADMAP

Q1/2 2017

• Sequence domains in BioEddie

• Library manager tool

• Oracle support

• KNIME/PP nodes (experimental)

Q3/4 2017

• ADC support in BioEddie

• Genealogy tracking

• Entity batches

• Sequence similarity search

Roadmap

THANK YOU

Roland Knispel

BIOMOLECULES IN R&D INFORMATICS - ChemAxon...More on this by Jarrod Medeiros, IDBS IDBS EWB Web...

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