ChemAxon’s consulting services has undergone substantial growth in the last several years. We now utilize talent from across the globe, servicing a wide range of project needs. From small short term solutions to mega-pharma project management, small-scale software integration/migration to customized product development. This presentation will cover some of the range of projects we are engaged in with some focus on a large web portal project we delivered for the European Lead Factory.

1. Consultancy Services
Informatics Pick-n-Mix
Erin Bolstad

2. Global Consulting Team
Skills, Resources, Experience:
● Project Management
● Solutions/packaging
● Customizations/Integration of
existing/3rd party software
● Rich scientific background
● Software design and development
(Java, Groovy, JS, .NET, mobile, etc.)
● Toolkit development (ETL, DSL, API,
ORM, etc)
Consultants
AppScis
Dedicated consulting
developers
Consultants
AppScis
Developers (100+)
Dedicated consulting
developers
Hungary
USA
Czech
Republic
Argentina

3. Project Examples
● Migrations: database migration, PM of customized development, form and data-access design,
customized training.

4. Project Examples
● Migrations: database migration, PM of customized development, form and data-access design,
customized training.
● Customized developer and end-user training

5. Project Examples
● Migrations: database migration, PM of customized development, form and data-access design,
customized training.
● Customized solutions: thin clients, integration of existing and in-house tech
● Customized developer and end-user training

6. DuPont Doc2DB Database
● System to trawl DuPont ELN + stored documents (PDF, Doc, etc)
● WebApp for complex queries
● Based on Doc2DB technology

9. Novartis Reactions Database
● Reactions data warehouse
o Import from various legacy databases (ISIS)
o Live feed from CambridgeSoft ELN
● Database migration: ISIS -> ChemAxon
● CambridgeSoft ELN chemistry -> ChemAxon
● AJAX-style web application providing query and filtering capabilities
● Web services interface for fitting into SOA

11. Project Examples
● Migrations: database migration, PM of customized development, form and data-access design,
customized training.
● Customized solutions: thin clients, integration of existing and in-house tech
● Spotfire integration (GSK)
● Customized developer and end-user training

14. Project Examples
● Customized project incubator
● Migrations: database migration, PM of customized development, form and data-access design,
customized training.
● Customized solutions: thin clients, integration of existing and in-house tech
● Spotfire integration (GSK)
● Customized developer and end-user training

15. Customized Product Incubator
Compound Registration
● Customizable business rules
○ Tautomers, solvents, isotopes,
formulations, alternate
identifications
● Salt and solvent multiplicity
● Templated bulk registrations
● API for updating downstream
processes, integrating to other
products (like ELN)
● Sits on database with thin client
interface - IT required
● Enterprise level: 1000’s of users

16. MiniReg
Customized Product Incubator
● Simple compound registration system sitting
within IJC. No IT overhead or support needed.
● Chemistry handling
○ Single salts
○ Batches
○ Samples Properties
● Biology assay handling
○ Aggregation at db level
● Highly customizable at database level
● Small - medium companies
(currently in ~10 companies)

17. Project Examples
● Customized project incubator
● Migrations: database migration, PM of customized development, form and data-access design,
customized training.
● Customized solutions: thin clients, integration of existing and in-house tech
● Spotfire integration (GSK)
● Customized developer and end-user training
● Large scale global project management

18. Large Scale PM for Global Pharma
● GSK: IJC rollout as a global reporting tool, assisted/trained,
customization of IJC, additional admin software creation. (3+ yrs)
● BMS: IJC customization/development for global roll-out needs,
training, migration of data, consulting on data-mart integration. Thin
client development. (2+ yrs)

19. Project Examples
● Customized project incubator
● Migrations: database migration, PM of customized development, form and data-access design,
customized training.
● Customized solutions: thin clients, integration of existing and in-house tech
● Spotfire integration (GSK)
● Customized components of large initiatives (OIDD, IMI)
● Customized developer and end-user training
● Large scale global project management

20. European Lead Factory is part of IMI
● Innovative Medicines Initiative
● http://www.imi.europa.eu/
IMI supports collaborative research
projects and builds networks of
industrial and academic experts in
order to boost pharmaceutical
innovation in Europe.
Part of Framework 7
Approx 25 projects covering many
aspects of healthcare, also
including:
● eTox
● Open PHACTS

21. European Lead Factory
EFPIA members
AZ
Bayer
Lundbeck
Janssen
Merck KGaA
Sanofi
UCB
SME members
BioAscent
ChemAxon
Edelris
GABO:mi
Lead Discovery Center
Merachem
Pivot Park Screening
Centre
Sygnature Discovery
Syncom
Taros Chemicals
TI Pharma
Academic members
University of Dundee
Leiden University
Max Planck Institute of Molecular Physiology
Netherlands Cancer Institute
Radbound University, Nijmegen
University of Groningen
Technical University of Denmark
University of Duisburg-Essen
University of Leeds
University of Nottingham
VU University Amsterdam
An alliance of participants collaborating on
identifying novel leads

22. ELF philosophy
Novel
Leads
Novel
Compounds
300,000 from EFPIA
members internal
collections
200,000 from newly
synthesized libraries
Novel
Screens

23. 13 Work packages
1. Programme Recruitment HTS
2. Compound Logistics
3. Assay Development
4. High Throughput Screening
5. Hit Characterisation
6. Medicinal Chemistry
7. Publication Policy / External Relations
8. Information Technology
9. Sourcing chemical library proposals
10. Review/selection of chemical library proposals
11. Experimental Validation
12. Library Production
13. Project Management

24. Library generation workflow
Crowdsourcing Consortium participant
Library selection committee
Assessed on:
1. Molecular properties
2. Structural features
3. Novelty
4. Diversity potential
5. Synthetic tractability
6. Innovative design
Experimental validation Design optimisation
Library production

25. Architecture
2 x Intel(R) Xeon(R) CPU E5-2620 v2 @ 2.10GHz (2 x 6 core + HT)
64GB RAM
Tomcat 7 MySQLFilesystem
Web App
Web
Browser Workflow engine
Job queuing system
Document store
Report generation
Automated email notification
Role management
Dynamically generated UI

26. Workflows and Roles
Three workflows for different types of user:
1. Consortium member
2. Non-EU/EAA citizen
3. EU/EAA citizen
Supported by workflow engine
Different levels of access
1. Submitter
2. LSC member
3. LSC Chair
4. ….
UI dynamically generated to ensure that you
only see what you’re supposed to see and
only do what you’re supposed to do

27. Step 1: registration
Users register themselves and
provide personal and affiliation
details

28. Step 2: enter library
Define your library in one of three ways:
1. Upload SDF
2. Upload MRV with Markush library
3. Pick R-groups from within pre-defined lists
and Markush Enumeration is used to
generate the library
Sketch scaffold with Marvin JS
Give it a title
Provide accompanying info including rationale and
synthesis validation info

29. Step 3: initial property
calculations
SSS for scaffold against reference set of 12M
structures using JChem Search
Exact match search for enumerated structures
against reference set of 12M structures
Property distributions of enumerated structures.
Properties generated with Chemical Terms
expressions with Calculator Plugins
Checking enumerated structures against UK MDA
legislation database from Compliance Checker
Matching enumerated structures against sets of
SMARTS filters provided by EFPIA members using
Chemical Terms match() and matchCount()
functions

30. Step 4: submit library
Further round of property calculations performed
and library now visible to Library Selection
Committee for consideration
At this stage user has handed over ownership of the
library idea to the European Lead Factory

31. Step 5: final property calculations
ECFP4 fingerprint
comparison with 12M
structures from reference
set
Fuzzy Pharmacophore fingerprint
comparison with 12M structures
from reference set
Generate histogram of most similar
structure in reference set for each
compound in the library.
~1000 x 12M x 2 comparisons.
“Old” molecular descriptor tables:
● For each search read descriptors from
database -> very IO bound.
● Single threaded.
● -> days for completion
“New” fast similarity search:
● Descriptors generated as binary file.
● Read into memory once
● Search fully multi-threaded.
● -> minutes for completion
● (1M x 1M completes in ~25 min)

32. Step 6: assessment
Approve Reject
Refine
Library Selection Committee

33. Status summary
"The Library Selection Committee has been using the web tool since the
start of 2014 to support the selection of library proposals. Since then, well
over 100 library proposals have been considered, around 80 of which have
been approved for synthetic validation. The procedure for assessing and
processing the proposals has been straightforward. The tool has allowed
the proposals to be handled confidentially and to be assessed rigorously; it
has saved huge time for both library proposal submitters and members of
the Library Selection Committee."
Adam Nelson
Chair Library Selection Committee

34. ChemAxon and Open Innovation

35. Professional Services (BINGO!)
● Product development
● Product customization
● Product Integration
● Workflow design/management
● Project management
● Creative solutions