Dear All,
I would like to circulate some current Cheminformatics- (and related) news to everyone as follows – in particular, our dates for 2025 have just been fixed, hence – mark your calendar!
The dates are as follows: 19 February, 23 April (note: shifted from 30 April), 3 September and 12 November 2025 – as usual, please see https://www.c-inf.net for the schedule, upcoming events, etc.
Also – Twitter/X ain’t no more (at least not really), but Bluesky is; feel free to follow me there for future announcements etc., happy to follow back: https://bsky.app/profile/andreasbender.bsky.social
So here we go …
Events
16th January 2025
7th International Mini-Symposium on Molecular Machine Learning (MML)
Virtual Event
https://www.uni-muenster.de/Chemie.oc/glorius/symposium_mml.html
27-31 January 2025
Virtual Winter School on Computational Chemistry
Virtual Event
https://www.winterschool.cc
29 January 2025
Biologics by Design Europe (by CCG)
Virtual Event
https://www.chemcomp.com/en/Biologics-2025-Europe.htm
19 February 2025
Cambridge Cheminformatics Meeting
Cambridge, UK and Virtual (Hybrid) – if you wish to present please get in touch!
https://www.c-inf.net
3 March 2025
BMCS 2nd Conformational Design in Drug Discovery 2025
Cambridge, UK
https://www.rscbmcs.org/events/conformationaldesign25
10-11 March 2025
CDK User Group Meeting
Maastricht, The Netherlands
https://www.linkedin.com/feed/update/urn:li:activity:7258924021394587649
6-9 April 2025
19th EFMC Short Course on Medicinal Chemistry (on AI)
Leiden, The Netherlands
http://www.efmcshortcourses.org
9-10 April 2025
Assay Guidance Workshop for High-Throughput Screening and Lead Discovery
Berlin, Germany
https://ncats.corsizio.com/event/66f2d5e6960282a2f3620b4d
28 July – 2 August 2025
Pre-Doctoral Research School: Emerging Research Trends in Computer Science
Saarbruecken, Germany
https://cmmrs.mpi-sws.org
Jobs
Head of CADD
Novartis
Basel, Switzerland
https://novartis.wd3.myworkdayjobs.com/Novartis_Careers/job/Basel-City/Head-of-CADD–Computer-Aided-Drug-Discovery-_REQ-10034233-1
Assistant Professor of Computational Molecular Biology
UC San Diego
San Diego, CA
https://apol-recruit.ucsd.edu/JPF04110
Computational Chemist, Cheminformatics Engineer, other roles
SandboxAQ
Remote, USA and Remote, Europe
https://www.sandboxaq.com/job-openings
Principal Scientist, Machine Learning
Prescient Design / Roche
Basel, Switzerland
https://roche.wd3.myworkdayjobs.com/roche-ext/job/Basel/Principal-Scientist–Machine-Learning_202411-129178-2
Lead Computational Chemist; Metabolomics Data Analyst
Pangea Bio
London, UK and Berlin, Germany
https://www.pangeabio.com/people/careers
Principal Scientist – Computational Chemistry
Amgen
San Francisco, CA
https://careers.amgen.com/en/job/south-san-francisco/principal-scientist-computational-chemistry-amgen-san-francisco/87/72534255632
Research Scientist, Senior Researcher Virtual Screening, other roles
Qubit Pharmaceuticals
Paris, France
https://www.linkedin.com/company/qubit-pharmaceuticals/jobs
Professorship Machine Learning in the Life Sciences
Medical University Vienna
Vienna, Austria
https://www.meduniwien.ac.at/web/karriere/offene-stellen/professuren/professur-machine-learning-in-the-life-sciences
Senior/Principal Scientist, Computational Chemistry/CADD
Ridgeline Discovery
Basel, Switzerland
https://careers.ridgelinediscovery.com/jobs/JCOBAKt3ZP1p/senior-scientist-principal-scientist-computational-chemistry-cadd
(Senior) Director for Scientific Digital Capabilities
Novo Nordisk
Malov,Denmark
https://www.linkedin.com/comm/jobs/view/4104815778
Postdoc Generative AI in Drug Discovery
Eindhoven University
Eindhoven, The Netherlands
https://www.linkedin.com/jobs/view/4107432139
Cheminformatics…
Practically significant method comparison protocols for machine learning in small molecule drug discovery
https://chemrxiv.org/engage/chemrxiv/article-details/672a91bd7be152b1d01a926b
It’s a long path we are on… but one we need to take
MAINFRAME
https://aircheck.ai/mainframe
‘MAINFRAME is an international network of machine learning scientists and computational chemists, dedicated to advancing pre-competitive drug discovery research. Members of MAINFRAME focus on developing open-source algorithms and predictive machine learning models of chemical bioactivity.’
ROBERT: Bridging the Gap Between Machine Learning and Chemistry
https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.1733
‘We introduce ROBERT, a software carefully crafted to make ML more accessible to chemists of all programming skill levels, while achieving results comparable to those of field experts’
Why some organic molecules have a color: Correlating optical absorption wavelength with conjugated bond chain length
https://bertiewooster.github.io/2024/10/15/Color-from-Conjugation.html
Nice tutorial, integrating chemistry and explanation with a Colab notebook
MCSview
https://mcsview.com
‘The fastest way to visualize maximum common substructures’
Cambridge Cheminformatics Meeting, 14 November 2024 – Recording online
https://youtu.be/wjrH-QAXBz0
On Molecular Hypershape Recognition and Crystal Structure Analysis
molli: A General Purpose Python Toolkit for Combinatorial Small Molecule Library Generation, Manipulation, and Feature Extraction
https://pubs.acs.org/doi/10.1021/acs.jcim.4c00424
‘We introduce the MOLecular LIibrary toolkit, “molli”, which is a Python 3 cheminformatics module that provides a streamlined interface for manipulating large in silico libraries’
Accurate RNA 3D structure prediction using a language model-based deep learning approach
https://www.nature.com/articles/s41592-024-02487-0
now also RNA … using RhoFold+
Uni-GBSA: an open-source and web-based automatic workflow to perform MM/GB(PB)SA calculations for virtual screening
https://academic.oup.com/bib/article/24/4/bbad218/7199492
‘Here, we introduce Uni-GBSA, a user-friendly automatic workflow to perform MM/GB(PB)SA calculations, which can perform topology preparation, structure optimization, binding free energy calculation and parameter scanning for MM/GB(PB)SA calculations’
Learning on compressed molecular representations
https://pubs.rsc.org/en/content/articlelanding/2024/dd/d4dd00162a
‘We show that the method can achieve performance competitive with chemical fingerprint- and GNN-based methodologies in general, and perform better than comparable methods on quantum chemistry and protein–ligand binding affinity prediction tasks’
Addressing Data Leakage in Computational Drug Design
https://www.linkedin.com/posts/rebecca-buller-blomberg-99556677_proteindesign-drugdiscovery-machinelearning-activity-7272551329217077248-N84L
One of the eternal topics in ML
ShEPhERD: Diffusing shape, electrostatics, and pharmacophores for bioisosteric drug design
https://arxiv.org/abs/2411.04130v1
‘We demonstrate ShEPhERD’s potential for impact via exemplary drug design tasks including natural product ligand hopping, protein-blind bioactive hit diversification, and bioisosteric fragment merging.’
https://github.com/coleygroup/shepherd
https://github.com/coleygroup/shepherd-score
Computational Care
https://www.science.org/content/blog-post/computational-care
… and the response …
https://www.linkedin.com/posts/gcorso_you-may-have-seen-a-recent-pre-print-1-ugcPost-7271633315235872769-YEoG
… and the response(s) to the response
https://www.linkedin.com/pulse/my-response-pat-walters-9rbde
https://www.linkedin.com/pulse/more-response-diffdockdiffdock-l-ajay-jain-w4ezc
Polarishub ADMET and bioactivity competitions
https://polarishub.io/competitions
‘Polaris makes it easy for the machine learning in drug discovery community to share and access datasets & benchmarks’
FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction
https://arxiv.org/abs/2412.10966
Structure-aware generative molecular design: from 2D or 3D?
https://cheminformantics.blogspot.com/
Blog post by Morgan Thomas
… beyond cheminformatics …
Larvol Sigma Database
https://sigma.larvol.com
Very useful drug/disease/trial database
CIPsee
https://cipsee.com/home
‘A new Chemical Intellectual Property lens to search, analyse and expand molecules in patent documents’
Pylustrator
https://pylustrator.readthedocs.io/en/latest
‘Pylustrator is a software to prepare your figures for publication in a reproducible way’
How to learn about biotech and pharma
https://www.linkedin.com/pulse/how-learn-biotech-pharma-frank-s-david-othoe
Might be useful to those new to the field
Getting the Numbers Right in Medicinal Chemistry
https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cmdc.202400620
The 21st Annual Wiley Prize in Biomedical Sciences
https://www.youtube.com/watch?v=75um91Stsbw
Interesting talk on the R&D leading to cystic fibrosis treatments
16 network visualization tools that you should know
https://medium.com/@vespinozag/16-network-visualization-tools-that-you-should-know-2c26957b707e
The antibodies don’t work! The race to rid labs of molecules that ruin experiments
https://www.nature.com/articles/d41586-024-03590-0
‘At that point, I wanted to leave science — because if things are really this unreliable, what’s the point?’
Limits for Learning with Language Models
https://arxiv.org/abs/2306.12213
Might also be useful to some
Atlas Venture 2024 Year In Review
https://lifescivc.com/2024/11/atlas-venture-2024-year-in-review
My favourite line: “Novo Nordisk is expected to drive 50% of GDP growth of Denmark in 2024′
Behind the scenes of getting to a tech transfer agreement with your university
https://scientistentrepreneurs.substack.com/p/behind-the-scenes-of-getting-to-a
The “AI Outperforms Doctors” Claim Is False, Despite NYT Story – A Rebuttal
https://sergeiai.substack.com/p/the-ai-outperforms-doctors-claim
From the series: ‘It’s not true just because it’s published’
ECBD: European chemical biology database
https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae904/7832351
Database with EU-OpenScreen data
SnapShot: Timescales in Cell Biology
https://www.sciencedirect.com/science/article/pii/S0092867416302082
Some are shorter, some are longer
Broad Institute ML in Drug Discovery Symposium – Recording Online
https://vimeo.com/event/4621282
For program see https://www.broadinstitute.org/machine-learning-drug-discovery-symposium/machine-learning-drug-discovery
Some questions about biotech that I find interesting
https://atelfo.github.io/2024/04/01/biotech-questions.html
by Alex Telford (and I also find them quite interesting!)
Genetic variation across and within individuals
https://www.nature.com/articles/s41576-024-00709-x
Questionable practices in machine learning
https://arxiv.org/pdf/2407.12220v1
Obviously this goes far beyond cheminformatics
Mistakes from my Failed Startup in Scalping Concert Tickets
https://datastream.substack.com/p/mistakes-from-my-failed-startup-in
Every start-up is different, you improvise day by day
WCAIR Organic Chemistry Padlet
https://uod.padlet.org/cgraebin0011/wcair-organic-chemistry-padlet-uz69z1wosstpcrz1
Contains quite some useful information
How to… DMPK series
‘https://wcair.dundee.ac.uk/training/training-resources/howto
This series will cover common in vitro drug metabolism and pharmacokinetic (DMPK) experiments. This series of animated videos will take you through the basic principles on how to set up, perform and analyse any given assay.’
Grit or quit: the power to walk away
https://www.linkedin.com/pulse/grit-quit-power-walk-away-mike-rea-hvmie
Decision making ain’t easy (and it’s often biased towards ‘hanging in there’)
… and clearly beyond cheminformatics
On ‘connected experiences’ of Microsoft products (e.g. Word)
https://www.linkedin.com/posts/johan-cedmar-brandstedt-a77b311_degenerativeai-createdontscrape-activity-7262514400987602945-ceEC
Sorry Human, You’re Wrong
https://engineeringprompts.substack.com/p/sorry-human-youre-wrong
Good luck when ‘AI’ takes over the world
On Google’s Willow Quantum Computer, vs the Maillard Computer
https://www.linkedin.com/posts/prof-todd-austin_quantum-quantumcomputing-benchmarking-activity-7272356364662775808-Ucmm
Age Normalized Testosterone Peaks at Series B for Male Startup Founders
https://arxiv.org/abs/2411.03361
So better don’t do Series C then
Using sequences of life-events to predict human lives
https://www.nature.com/articles/s43588-023-00573-5
No comment
AI Death Calculator
https://crushon.ai/character/cdc77abe-83ba-4b64-8e35-005ab8bd2af0/details
Good to know
How to (not) do your daily stand-up
https://www.linkedin.com/posts/ivett-%C3%B6rd%C3%B6g-03aa9035_if-this-is-your-daily-meeting-stop-no-ugcPost-7264664276236173312-Vi2A
Guess that applies to many meetings
Humphrey’s world: how the Samuel Smith beer baron built Britain’s strangest pub chain
https://www.theguardian.com/news/2024/dec/19/humphreys-world-how-the-samuel-smith-beer-baron-built-britains-strangest-pub-chain
Bit of a different approach from ‘Spoons it seems
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.
I wish everyone a good Christmas/Holiday Period, and all the best for 2025!
See you again next year,
Andreas