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Cambridge Cheminformatics Newsletter, March-May 2024

Dear All,

I would like to circulate some current Cheminformatics- (and related) news to everyone as follows.

In particular please note our next Cambridge Cheminformatics Meeting on 8 May (Wednesday next week), as usual hybrid at the CCDC and via Zoom, with details given below.

So here we go…


6 May 2024
Machine Learning for Drug Discovery
Vienna, Austria

8 May 2024, 4pm UK time
Cambridge Cheminformatics Meeting
Cambridge, UK and Virtual (Hybrid)
More details:
Direct Zoom registration:–hqj0qGtaAUInFkoKdTqxuH8n2rYZd


Ligand-based 3D Pharmacophore Search for Drug Analogues in Ultra-Large Combinatorial Libraries
Modest von Korff
Alipheron AG –

Creative Ways to Get Wet Lab Scientists and Data Scientists to Work Closer Together – Ideas & Discussion
Raminderpal Singh
Hitchhikers AI –

CMD + V for Chemistry: Image to Chemical Structure Conversion Directly Done in the Clipboard
Oliver Schilter
EPFL/IBM Zurich –

Everyone is welcome – please join in and circulate further!

9 May 2024
CCDC Innovation in Discovery Science – UGM 2024
Virtual Event

28 May 2024
EFMC2 Tandem Talk: ‘Accelerating Lead Optimisation by Constantly Rebuilding Free Wilson Models Using Automated Core Finding in Anti-Viral Drug Discovery’
Virtual Event

10-14 June 2024
Spring School Structure-based Computer-aided Drug Design
Lausanne Switzerland

14 June 2024
Molecular Simulations for Chemistry
London, UK

18/19 June 2024
Cresset User Group Meeting 2024
Brussels, Belgium

24-28 June 2024
Generative Modeling Summer School
Eindhoven, The Netherlands

1-3 July 2024
CCPBioSim Annual Conference
Newcastle, UK

2/3 July 2024
7th Machine Learning and AI in Bio(Chemical) Engineering Conference
Cambridge, UK
(abstract submission open until 5 May)

9-13 September 2024
2nd International Summer School AI4MedChem
Muenster, Germany

11-13 September 2024
Zurich, Switzerland

11-13 September 2024
Computational Molecular Science 2024
University of Warwick

16-18 September 2024
7th Artificial Intelligence in Chemistry Symposium
Cambridge, UK
(oral abstracts open until 12 April/posters until 3 May)

17-20 September 2024
AI in Drug Discovery Workshop at ICANN24
Lugano, Switzerland

Job Seekers

I’m looking for my next role, potentially in Sales/BD. I have 10+ yrs sales experience, including taking Watson Genomics to market in the US for IBM (2012-2015) and as VP of Sales for Eagle Genomics (2015-2018). I founded and am just exiting as CEO of an early stage AI biotech (Incubate Bio, applying Causal Inference). In addition, I recently launched and currently lead – a global non-profit community, accelerating the use of AI/GenAI in drug discovery. For more about me:  Please contact me on LinkedIn or at


Tenure Track Assistant Professor Computer-Aided Drug Design
University of Groningen
Groningen, The Netherlands

Senior Drug Hunter
Paris, France

Executive Director, Structural Biology
Oxford, UK

Investigator, Cheminformatics
Stevenage, UK

Lead Cheminformatics Machine Learning Data Scientist
London, UK

Senior Scientist, AI/ML Cheminformatics
San Francisco, CA

Drug Discovery Lead – AI in PROTAC Development
Eschborn, Germany

Scientist or PostDoc in Cheminformatics
Schalkham, Germany

Postdoctoral Fellow on Biological Data Sciences
IRB Barcelona
Barcelona, Spain

Postdoc, Computer-Aided Drug Design
Institut Pasteur
Paris, France

Postdoctoral Research Associate – Cheminformatics/Computational Toxicologist
UNC Chapel Hill
Chapel Hill, NC

Postdoc Integrative Data Analysis/Cell Morphology Analysis
Uppsala University
Uppsala, Sweden

PostDoc Cheminformatics
IPB Leipzig
Leipzig, Germany

Research Associate in AI for Chemistry
Imperial College London
London, UK

PhD Student in ‘Digital Chemistry’
Wuppertal University
Wuppertal, Germany


ELN (Electronic Lab Notebook) Finder
“The ELN Finder helps you to search and select a suitable Electronic Lab Notebook (ELN) for your purposes”

Combining IC50 or Ki Values from Different Sources Is a Source of Significant Noise
… so don’t just plug everything together to ‘make it bigger’

‘FragGrow is a web server for structure-based drug design by fragment growing’

‘Faerun facilitates the creation of interactive (2D and 3D) HTML plots of chemical data (or chemical spaces)’

Recording of the Cambridge Cheminformatics Meeting from 21 February 2024 is now online – topics covered are MolFlux, Reaction Extraction, Machine Learning for Synthetic Chemistry

PlayMolecule Viewer: A Toolkit for the Visualization of Molecules and Other Data
‘PlayMolecule Viewer is a web-based data visualization toolkit designed to streamline the exploration of data resulting from structural bioinformatics or computer-aided drug design efforts’

DockOpt: A Tool for Automatic Optimization of Docking Models
‘To make docking more accessible, we developed a new utility called DockOpt, which automates the creation, evaluation, and optimization of docking models prior to their deployment in large-scale prospective screens’

‘In continuation of the established SAMPL challenges, the first euroSAMPL blind prediction challenge investigates the ability of computational methods to predict acidity constants (pKa) of 35 drug-like small molecules’

Structure is beauty, but not always truth
… visuals (as words) steer your mind, but make sure you get steered into the right direction

CMD + V for chemistry: Image to chemical structure conversion directly done in the clipboard
(Oliver is also presenting in the Cheminformatics Meeting next week, please see above)

AiZynth impact on medicinal chemistry practice at AstraZeneca
Predicting synthesis – and examples of impact

Will the real INS018_055 please stand up?
Blog post by Chris Southan about the long road of digging up a chemical structure of interest from patents

… beyond cheminformatics …

The JUMP-Cell Painting Consortium data has recently been released

It’s Been a Decade of AI in the Drug Discovery Race. What’s Next?
Review of the pipelines of some of the larger AI-driven drug discovery companies

Patterns in Practice
‘Patterns in Practice is an AHRC funded project that is exploring how practitioners’ beliefs, values and feelings interact to shape how they engage with and in data mining and machine learning’, one of areas included is ‘mining chemical data to inform drug discovery in the pharmaceutical industry’

All models are wrong and yours are useless: making clinical prediction models impactful for patients
Florian Markowetz on the difference between theory in practice, in the clinical prediction context

‘Open-source enablement that comes with a community, leveling the AI playing field and enabling drug discovery’

‘AI in Drug Discovery: When, Where, and How Much?’
Presentation by Derek Lowe on the above topic

Dense grid searches over neural network hyperparameters…
… look like the beauty, but they are the beast

Quality criteria for degraders – Probing biology with a novel modality
Presentation by Ingo Hartung

Evaluation of clinical prediction models (part 1): from development to external validation
… about clinical data, but the fields aren’t that different after all, so there are learnings in there for everyone

… and clearly beyond cheminformatics

Science in the age of selfies
Very true… and even since 2016 we have probably moved further into this direction

Scientists turn to AI to make beer taste even better
If you ever doubted the impact of ‘AI’ – here is the key proofpoint!

Users Say Microsoft’s AI Has Alternate Personality as Godlike AGI That Demands to Be Worshipped
… but who doesn’t want to have a ‘godlike AGI’ anyway!

AI applied to the illustration of scientific articles
… and as we can see use cases of generative AI are endless!

Great, Now Write an Article About That: The Crescendo Multi-Turn LLM Jailbreak Attack
… another way to ‘break’ LLMs

A moment that changed me: I patronised a refugee – and he taught me an invaluable lesson
On the danger of assumptions, and how everyone can learn from everyone

Sagrada Familia in Barcelona ‘will be completed in 2026’
I find this idea honestly _very_ strange

Match Group and Managed Dissatisfaction
Worthwhile read on how well-known companies evolved (and why)

How an epic climb lifted one woman out of life’s lowest point
Yep, there is a life away from the computer (but don’t trust everything you find on the Interweb please!)

I believe this is all from my side for now – if you have any information for me to circulate, or wish to present at one of our next Cambridge Cheminformatics Meetings, please just let me know, cheers!

Best wishes,


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