Dear All,
I would like to circulate some current Cheminformatics- (and related) news to everyone as follows – in particular, our next Cambridge Cheminformatics Meeting will take place on 3 September (Wednesday next week), as usual in hybrid mode at the CCDC and on Zoom, for details please see below.
So here we go…
Events
3 September 2025, 4pm (UK)
Cambridge Cheminformatics Meeting
Cambridge Crystallographic Data Centre, Cambridge, UK and Online (Hybrid Mode)
Direct registration for remote participation: https://cam-ac-uk.zoom.us/meeting/register/LHvD0pJ9RROvIL5IfHAEWg
More Information: https://c-inf.net
Programme
Innovation in Pharma
Mike Rea, IDEA Pharma
https://www.ideapharma.com
Cross Multimodality Learning of Cell Painting and Transcriptomics data for Small Molecule Activity Prediction
Son Ha, Johannes Gutenberg University Mainz
https://www.datamining.informatik.uni-mainz.de/son-ha
Datagrok: A Swiss-Army Knife for Cheminformatics
Andrew Skalkin, Datagrok
https://datagrok.ai
15-18 September 2025
AI2050 AI/ML Tools for Drug Discovery Webinar Series
Virtual event, targeted primarily towards participants in the Global South
https://docs.google.com/forms/d/e/1FAIpQLSclS51b3SZ0I6NWQ9bu3iH9QRlrjjgNXqgx7dF_awODTX3z8g/viewform
Course material: https://ersilia.gitbook.io/ersilia-book/training-materials/ai2050-ai-for-drug-discovery
30 September 2025
5th Virtual ChemBioTalks
Virtual event
https://web.cvent.com/event/60e9f372-d2fd-49f0-bad4-10ac9a71b11c/summary
15 October 2025
Drug Safety Forum 2025
London, UK
https://www.apconix.com/drug-safety-forum-2025-current-and-future-opportunities-for-improving-translational-safety
16 October 2025
Discngine Meetup Vol. 5: Peptide Discovery
Virtual Event
https://event.discngine.com/discngine-meetup-vol-5-peptide-discovery
7 November 2025
Machine Learning in Drug Discovery Symposium
Cambridge, MA and online (hybrid)
https://www.broadinstitute.org/machine-learning-drug-discovery-symposium/machine-learning-drug-discovery
Vacancies
Pharmacokineticist, PK/PD Modelling & Simulation (and other vacancies)
Lundbeck
Copenhagen, Denmark
https://www.linkedin.com/jobs/view/4288929365
Postdoctoral Fellowship
EBI, ChEMBL group
Hinxton, UK
https://chembl.blogspot.com/2025/07/invite-to-apply-for-arise2-postdoctoral.html
Associate Director, Cheminformatics
Takeda
Boston, MA
https://www.linkedin.com/jobs/view/4285552121
Computational Chemist & Cheminformatics Scientist
Continental
Lousado, Portugal
https://www.linkedin.com/jobs/view/4264707482
Research Scientist ML, PKPD Modelling Lead (and other vacancies)
Isomorphic Labs
London, UK and Lausanne, Switzerland
https://www.linkedin.com/jobs/view/4085314773
https://www.linkedin.com/jobs/view/4278079253
Postdoc Position: Chemical and Protein Language Models (position open until filled)
Saarland University
Saarbruecken, Germany
https://groups.google.com/g/ml-news/c/pMY8W0jIyCY/m/ByXqCOhbAQAJ
Cheminformatician
Variational AI
Vancouver, Canada (or remote)
https://variational.ai/jobs/cheminformatician
Machine Learning Engineer (and other vacancies)
Altos Labs
San Diego, CA
https://www.linkedin.com/jobs/view/4243341779
Senior/Staff Computer Aided Drug Design Scientist
Chemify
Glasgow, United Kingdom
https://www.linkedin.com/jobs/view/4280912897
Data Engineer, ML Infrastructure Engineer
CuspAI
Cambridge, UK
https://www.linkedin.com/company/cusp-ai/jobs
Research Scientist – Chem Bio
AI Security Institute
London, UK
https://job-boards.eu.greenhouse.io/aisi/jobs/4548437101
Scientist in Small Molecule CADD (and other roles)
Roche
Basel, Switzerland (and other locations)
https://www.linkedin.com/jobs/view/4278053153
Software Engineer
Astex
Cambridge, UK
https://www.linkedin.com/jobs/view/4278783128
Head of Molecular Simulations, Principal Computational Chemist (and other roles)
Aqemia
Paris, France
https://www.linkedin.com/jobs/view/4236471039
https://www.linkedin.com/jobs/view/4261095869
Cheminformatics…
Electron flow matching for generative reaction mechanism prediction
https://www.nature.com/articles/s41586-025-09426-9
Reaction prediction ‘grounded in physics’
Directory of Computer-aided Drug Design Tools
https://click2drug.org
‘Click2Drug contains a comprehensive list of computer-aided drug design (CADD) software, databases and web services’, with currently 807 links
Video of the Cambridge Cheminformatics Meeting from 23 April 2025 online
https://www.youtube.com/watch?v=na0glshi0FI
Day in the Life of a Chief Data Science Officer; Flagging High-Risk Chemicals Without Full Identification; Narrowing the Gap Between Machine Learning Scoring Functions and Free Energy Perturbation Using Augmented Data
(Some of) the background leading to AlphaFold…
https://www.linkedin.com/feed/update/urn:li:activity:7345745870526541824
by Daniel Cremers
Novartis/DRUG-seq U2OS MoABox Dataset
https://zenodo.org/records/14291446
Transcriptomics data… still gives you good bang for the buck, thanks for making this available
Related: DRUG-Seqr
https://drugseqr.maayanlab.cloud
“Search through 26,316 gene sets from the Novartis/DRUG-seq U2OS MoABox Dataset”
Free Cheminformatics Web Tools for Medicinal Chemists
https://ertlmolecular.com
Peter Ertl’s free cheminformatics web tools
Identification of nanomolar adenosine A2A receptor ligands using reinforcement learning and structure-based drug design
https://www.nature.com/articles/s41467-025-60629-0
Including synthesis of novel active scaffolds, binding and functional evaluation, X-ray, NMR… well done, Morgan!
Cheminformatics Modules
https://hcd.rtpnc.epa.gov/#/utils
‘The Cheminformatics Modules [hosted by the EPA] is a set of prototype modules which are using a compilation of information sourced from many sites, databases and sources including U.S. Federal and state sources and international bodies that saves the user time by providing information in one location’
Evaluating Boltz-2 on Real Drug Targets: Does it work?
https://www.deepmirror.ai/post/boltz-2-real-drug-targets
In summary: Often yes for well-known and rigid targets; often no for less explored targets and those with lots of flexibility
Pat Walters also wrote about this topic: https://patwalters.github.io/Three-Papers-Demonstrating-That-Cofolding-Still-Has-a-Ways-to-Go
SMARTS.plus
https://chemist.smarts.plus
Ever need to name your heterocycles…? Go to SMARTS.plus!
… beyond Cheminformatics …
The Day Novartis Chose Discovery
https://www.alexkesin.com/p/the-day-novartis-chose-discovery
‘How a Swiss pharma giant built the last great corporate research skunkworks – and why that model may never work again’… I didn’t quite realize this all when I did my postdoc at NIBR many moons ago, but that doesn’t make me any less grateful for the time there
Artificial Intelligence, Scientific Discovery, and Product Innovation
https://arxiv.org/pdf/2412.17866
… ‘I show that AI automates 57% of “idea-generation” tasks, reallocating researchers to the new task of evaluating model-produced candidate materials’
… yeah well … just that MIT distances itself from it…
https://futurism.com/the-byte/mit-disavows-paper-ai-scientific-discoveries
There’s just so much progress in AI
AI, Materials, and Fraud, Oh My!
https://thebsdetector.substack.com/p/ai-materials-and-fraud-oh-my
as above
A do-or-die moment for the scientific enterprise
https://reeserichardson.blog/2025/08/04/a-do-or-die-moment-for-the-scientific-enterprise
Guess I gotta agree with this one
More details:
The entities enabling scientific fraud at scale are large, resilient, and growing rapidly
https://www.pnas.org/doi/10.1073/pnas.2420092122
Also related:
Explosion of formulaic research articles, including inappropriate study designs and false discoveries, based on the NHANES US national health database
https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3003152
Deep learning gets the glory, deep fact checking gets ignored
https://rachel.fast.ai/posts/2025-06-04-enzyme-ml-fails
‘When impressive AI biology results are full of errors’, aka the ‘Bullsh*t asymmetry principle’ – it takes 10 times more energy to refute an erroneous finding than to create (and publicise!) it
Global Innovation Index 2024
https://www.wipo.int/web-publications/global-innovation-index-2024/assets/67729/2000%20Global%20Innovation%20Index%202024_WEB3lite.pdf
I just checked a few countries I am somewhat familiar with and I can see some truths in it
‘With Sadness and Resolve: Why I Resigned as Chief Medical Officer of a National Institutes of Health Institute and What Comes Next’
https://royalsocietypublishing.org/doi/epdf/10.1098/rsos.160384
Artificial intelligence meets natural stupidity
https://dl.acm.org/doi/10.1145/1045339.1045340
(From April 1976, but still current)
Generalization bias in large language model summarization of scientific research
https://royalsocietypublishing.org/doi/10.1098/rsos.241776
Always make sure to look under the hood
Four Types of ‘Premature Scaling’ in Biotech
https://lifescivc.com/2011/09/four-types-of-premature-scaling-in-biotech
Bigger (and getting bigger) isn’t always better
CRMArena-Pro: Holistic Assessment of LLM Agents Across Diverse Business Scenarios and Interactions
https://arxiv.org/abs/2505.18878
‘Experiments reveal leading LLM agents achieve only around 58% single-turn success on CRMArena-Pro, with performance dropping significantly to approximately 35% in multi-turn settings’ (by Salesforce)
The Hater’s Guide To The AI Bubble
https://www.wheresyoured.at/the-haters-gui
On ‘The Magnificent 7’s Weak point: NVIDIA’, by Ed Zitron
AI: great expectations
https://people.csail.mit.edu/brooks/idocs/AI_hype_1988.pdf
by Rodney Brooks, March 1988
I’m Losing All Trust in the AI Industry
https://www.thealgorithmicbridge.com/p/im-losing-all-trust-in-the-ai-industry
‘As a supporter, I would love not to feel this way’
IC50 is a deep rabbit hole
https://blog.turbine.ai/p/ic50-is-a-deep-rabbit-hole
Not too dissimilar from other bio data I suppose
How reliable are public antibody-antigen datasets for model training?
https://www.linkedin.com/posts/iddo-weiner-b57594131_antibody-data-patents-activity-7345712207344599040-MIFw/
In short: Not very
HSBC Venture Healthcare Report
https://www.hsbcinnovationbanking.com/-/media/hinv/pdf/2025-midyear-venture-healthcare-report.pdf
Annotated History of Modern AI and Deep Learning
https://people.idsia.ch/~juergen/deep-learning-history.html
by Juergen Schmidhuber
AI for Good [Appearance?]
https://aial.ie/blog/2025-ai-for-good-summit
Commentary by Abeba Birhane
MLCB24 – Lecture01 – Introduction
https://www.youtube.com/watch?v=1zZSPeKGRzw
by Manolis Kellis; see also other parts
Applications of Portfolio Theory to Accelerating Biomedical Innovation
https://www.pm-research.com/content/iijpormgmt/51/1/213
The theory behind BridgeBio
Clinical Development Success Rates 2011-2020
https://www.bio.org/clinical-development-success-rates-and-contributing-factors-2011-2020
By disease area; see Figure 2 (which is actually a table) on page 7 of the PDF
Is Biopharma Doing Enough to Advance Novel Targets?
https://www.lek.com/insights/hea/us/ei/biopharma-doing-enough-advance-novel-targets
Everyone is working on the same targets… but of course there are also ‘good’ reasons for that
You People Made Me Give Up My Peanut Farm Before I Got To Be President
https://theonion.com/you-people-made-me-give-up-my-peanut-farm-before-i-got-1819585048/
Glad to hear US politics is so integer
The AI jobs crisis is here, now
https://www.bloodinthemachine.com/p/the-ai-jobs-crisis-is-here-now
Just in somewhat different ways than possibly expected
Large Language Models, Small Labor Market Effects
https://bfi.uchicago.edu/working-papers/large-language-models-small-labor-market-effects
Good to read some numbers and to stay on the factual level
… and clearly beyond Cheminformatics
A Case of Bromism Influenced by Use of Artificial Intelligence
https://www.acpjournals.org/doi/10.7326/aimcc.2024.1260
Real-World Impact of AI
GitHub’s Fall: Microsoft’s AI Takeover, Developer Betrayal, and the Next Fight for Digital Sovereignty
https://www.linkedin.com/pulse/githubs-fall-microsofts-ai-takeover-developer-betrayal-dion-wiggins-oyetc
We are Living in The Era of the AI Idiot
https://www.linkedin.com/pulse/we-living-era-ai-idiot-dion-wiggins-3ovwc
Leaked ChatGPT Conversation Shows User Identified as Lawyer Asking How to “Displace a Small Amazonian Indigenous Community From Their Territories in Order to Build a Dam and a Hydroelectric Plant”
https://futurism.com/leaked-chatgpt-lawyer-displace-amazonian
A use case showing the versatility of ChatGPT
compression culture is making you stupid and uninteresting
https://maalvika.substack.com/p/compression-culture-is-making-you
Don’t zip yourself too much
History repeats itself?
https://www.linkedin.com/posts/claessen_history-repeats-itself-activity-7362714688905723904-U3qM
… but it rhymes
Coordinated Universal Time: An overview
https://www.itu.int/hub/2023/07/coordinated-universal-time-an-overview
There is no ‘time’ as such… if someone ever asks me for ‘the time’ again I probably will feel entirely unable to answer the question
I was one of those men who couldn’t stop talking. Here’s how I learned to shut up and listen
https://www.theguardian.com/lifeandstyle/2025/jun/26/i-was-one-of-those-men-who-couldnt-stop-talking-heres-how-i-learned-to-shut-up-and-listen
Bit of an AI poem
https://www.linkedin.com/feed/update/urn:li:activity:7330651568297361409
‘AI is just another tool. Like a calculator.’ …
Accountability Sinks
https://250bpm.substack.com/p/accountability-sinks
The problem with accountability in large organizations
Google Scholar is manipulatable
https://arxiv.org/abs/2402.04607
Follow your incentives and … you can just do things!
Springer Nature book on machine learning is full of made-up citations
https://retractionwatch.com/2025/06/30/springer-nature-book-on-machine-learning-is-full-of-made-up-citations
Very good
How to Stop Bouncing Back Into Broken Systems
https://www.psychologytoday.com/us/blog/possibilitizing/202505/how-to-stop-bouncing-back-into-broken-systems
‘You don’t need more resilience, you need to stop normalizing the nonsense’
Systems are crumbling – but daily life continues. The dissonance is real
https://www.theguardian.com/wellness/ng-interactive/2025/may/22/hypernormalization-dysfunction-status-quo
I visited every country in the world without flying. Here are eight things I learned
https://www.theguardian.com/lifeandstyle/2025/apr/21/i-visited-every-country-in-the-world-without-flying-here-are-eight-things-i-learned
(Ages ago I tried to summarize a few things I learned from traveling in India as well: https://andygoesindia.blogspot.com/2013/08/what-india-taught-me.html)
Welcome to AirSpace – How Silicon Valley helps spread the same sterile aesthetic across the world
https://www.theverge.com/2016/8/3/12325104/airbnb-aesthetic-global-minimalism-startup-gentrification
Uruguay’s ex-President José Mujica, nicknamed ‘world’s poorest president,’ dies at 89
https://www.npr.org/2025/05/13/nx-s1-5288793/uruguay-jose-mujica-dies
Quite a life
In 1975, thousands of babies were daringly airlifted from the Vietnam war
https://www.aljazeera.com/features/2025/4/26/in-1975-thousands-of-babies-were-daringly-airlifted-from-the-vietnam-war
The Daily Reid: Lawless America
https://www.joyannreid.com/p/the-daily-reid-lawless-america
Deepfakes in recruitment…
https://www.linkedin.com/posts/roblesliesedicii_deepfake-ai-fraud-activity-7313508758788210689-NT9T
Recruitment doesn’t get easier…
I Made My Shed the Top Rated Restaurant On TripAdvisor
https://www.vice.com/en/article/i-made-my-shed-the-top-rated-restaurant-on-tripadvisor/
… but at least getting to the top of TripAdvisor does
Have the great British public forgotten how to queue in pubs?
https://www.independent.co.uk/voices/pubs-bar-single-file-queue-wetherspoons-b2545437.html
Finally we get to the important things in life
Related:
https://www.theguardian.com/news/video/2025/jul/22/last-orders-a-pub-crawl-across-the-uks-dying-booze-industry-video
Web3 is Going Just Great
https://www.web3isgoinggreat.com
We all knew that of course
Music Corner
Given I have worked on getting my life priorities straight in recent times I also have had time for a proper ‘music corner’ in this edition of the newsletter
Albums:
Cocteau Twins – Treasure (1984)
https://tidal.com/browse/album/49794652?u
Fantastic Album – I really had to stop work for an hour when I came across it to listen to this
Hugo Kant – Out of Time (2017)
https://tidal.com/browse/album/73046016?u
Excellent – especially ‘Entering the Black Hole’ and ‘Clouds’
Waxahatchee – Tigers Blood (2024)
https://tidal.com/browse/album/336429538?u
Ash – Self-Discovery (2024)
https://tidal.com/browse/album/320302907?u
Mirah – C’mon Miracle (2004)
https://tidal.com/browse/album/165271559?u
Beautiful guitars
Los Chikos del Maiz – La Estanquera de Saigon (2014)
https://tidal.com/browse/album/418450014?u
Perfect Album from Beginning to End (especially ‘La Estanquera de Saigon’ or ‘Revisionismo o Barbarie’, excellent hiphop/metal cross-over)
Keny Arkana – Entre ciment et belle etoile (2006)
https://tidal.com/browse/album/102245851?u
Redzed – Ecstasy (2017)
https://tidal.com/browse/album/444209035?u
My favourite Czech rapper, and my favourite album of him
Bon Iver – For Emma, Forever Ago (2008)
https://tidal.com/browse/album/25055553?u
Vladimir Kocibelli – My Feelings (Albanian Traditional Music) (1994)
https://tidal.com/browse/album/430479697?u
The Clash – London Calling (1979)
https://tidal.com/browse/album/21785493?u
Singles:
Youngblood Brass Band – Pastime Paradise
https://tidal.com/browse/track/20132022?u
My favourite variant of the various ‘Paradise’ riffs
Gallowstreet – Asterix
https://tidal.com/browse/track/146055572?u
More brass – one of their best songs IMO
Boogie Belgique – Stairway to the USSR
https://tidal.com/browse/track/53927906?u
Young MC – Principal’s Office
https://tidal.com/browse/track/33733326?u
Mon Amour – Naaman
https://tidal.com/browse/track/402662569?u
Beautiful song – Naaman just died from a brain tumor earlier this year, so enjoy things while they last
Ivo Dimchev – I Cure
https://tidal.com/browse/track/373382009?u
Greetings to Bulgaria
Doctor Flake – Cinema
https://tidal.com/browse/track/80928944?u
Friedrich Liechtenstein – Das Badeschloss
https://www.reddit.com/r/listentothis/comments/4jvsmx/friedrich_liechtenstein_das_badeschloss_made_for
(see also Belgique, Belgique https://tidal.com/browse/track/86552321?u)
Thomas Benjamin Wild Esq – I have no more fucks to give
https://tidal.com/browse/track/105610829?u
Straight to the bottom line I guess
And finally… from the series ‘affordable luxuries that simply make your life better’: Make sure to get a tube amplifier for your headphones, such as https://xduoo.net/product/ta-26s (excellent pairing with e.g. the Sivga SV023… of course ‘tube rolling’ is the next thing I need to explore now!)
I believe this is all from my side for now – as usual, if you have any information for me to circulate, or wish to present at one of our next Cambridge Cheminformatics Meetings, please just get in touch, cheers!
Best wishes,
Andreas
—
Andreas Bender, PhD