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…
Events
6 May 2024
Machine Learning for Drug Discovery
Vienna, Austria
https://www.mlfordd.com
8 May 2024, 4pm UK time
Cambridge Cheminformatics Meeting
Cambridge, UK and Virtual (Hybrid)
More details: https://www.c-inf.net
Direct Zoom registration: https://cam-ac-uk.zoom.us/meeting/register/tZUsc–hqj0qGtaAUInFkoKdTqxuH8n2rYZd
Programme
Ligand-based 3D Pharmacophore Search for Drug Analogues in Ultra-Large Combinatorial Libraries
Modest von Korff
Alipheron AG – https://alipheron.com/
Creative Ways to Get Wet Lab Scientists and Data Scientists to Work Closer Together – Ideas & Discussion
Raminderpal Singh
Hitchhikers AI – https://www.hitchhikersai.org/
CMD + V for Chemistry: Image to Chemical Structure Conversion Directly Done in the Clipboard
Oliver Schilter
EPFL/IBM Zurich – https://schwallergroup.github.io/people/oliver_schilter.html
Everyone is welcome – please join in and circulate further!
9 May 2024
CCDC Innovation in Discovery Science – UGM 2024
Virtual Event
https://info.ccdc.cam.ac.uk/discovery-science-ugm-2024
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
https://www.efmctandemtalks.org
10-14 June 2024
Spring School Structure-based Computer-aided Drug Design
Lausanne Switzerland
https://www.sib.swiss/training/course/20240609_CADD
14 June 2024
Molecular Simulations for Chemistry
London, UK
https://www.rsc.org/events/detail/78098/molecular-simulations-for-chemistry
18/19 June 2024
Cresset User Group Meeting 2024
Brussels, Belgium
https://www.cresset-group.com/about/events/cresset-user-group-meeting-2024
24-28 June 2024
Generative Modeling Summer School
Eindhoven, The Netherlands
https://gemss.ai/2024
1-3 July 2024
CCPBioSim Annual Conference
Newcastle, UK
https://www.ccpbiosim.ac.uk/newcastle2024
2/3 July 2024
7th Machine Learning and AI in Bio(Chemical) Engineering Conference
Cambridge, UK
(abstract submission open until 5 May)
https://www.mabc-cambridge.ai
9-13 September 2024
2nd International Summer School AI4MedChem
Muenster, Germany
https://www.uni-muenster.de/Chemie.pz/forschen/ag/koch/ai4medchem.html
11-13 September 2024
RDKit UGM
Zurich, Switzerland
https://www.eventbrite.com/e/13th-rdkit-ugm-2024-tickets-860637719587
11-13 September 2024
Computational Molecular Science 2024
University of Warwick
https://warwick.ac.uk/fac/sci/chemistry/chemevents/events/cms2024
16-18 September 2024
7th Artificial Intelligence in Chemistry Symposium
Cambridge, UK
(oral abstracts open until 12 April/posters until 3 May)
https://www.rscbmcs.org/events/aichem7
17-20 September 2024
AI in Drug Discovery Workshop at ICANN24
Lugano, Switzerland
https://e-nns.org/wp-content/uploads/2024/ICANN2024-AIDrugDis-CfP_final.pdf
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 HitchhikersAI.org – a global non-profit community, accelerating the use of AI/GenAI in drug discovery. For more about me: https://www.raminderpalsingh.com/. Please contact me on LinkedIn or at raminderpalsingh123@gmail.com.
Jobs
Tenure Track Assistant Professor Computer-Aided Drug Design
University of Groningen
Groningen, The Netherlands
https://www.linkedin.com/jobs/view/3852726917
Senior Drug Hunter
Aqemia
Paris, France
https://www.linkedin.com/jobs/view/3884465130
Executive Director, Structural Biology
Exscientia
Oxford, UK
https://apply.workable.com/exscientia/j/98241BEFD6
Investigator, Cheminformatics
GSK
Stevenage, UK
https://www.linkedin.com/jobs/view/3908299670
Lead Cheminformatics Machine Learning Data Scientist
BenevolentAI
London, UK
https://www.linkedin.com/jobs/view/3906034693
Senior Scientist, AI/ML Cheminformatics
Merck
San Francisco, CA
https://www.linkedin.com/jobs/view/3902167005
Drug Discovery Lead – AI in PROTAC Development
Innoplexus
Eschborn, Germany
https://www.linkedin.com/jobs/view/3876440694
Scientist or PostDoc in Cheminformatics
Empa
Schalkham, Germany
https://www.linkedin.com/jobs/view/3913621560
Postdoctoral Fellow on Biological Data Sciences
IRB Barcelona
Barcelona, Spain
https://recruitment.irbbarcelona.org/jobs/3626103-postdoctoral-fellow-on-biological-data-sciences-ref-pd-24-04
Postdoc, Computer-Aided Drug Design
Institut Pasteur
Paris, France
https://research.pasteur.fr/fr/job/postdoctoral-position-in-computer-aided-drug-design
Postdoctoral Research Associate – Cheminformatics/Computational Toxicologist
UNC Chapel Hill
Chapel Hill, NC
https://www.linkedin.com/jobs/view/3885231070
Postdoc Integrative Data Analysis/Cell Morphology Analysis
Uppsala University
Uppsala, Sweden
https://www.jobb.uu.se/details/?positionId=716991
PostDoc Cheminformatics
IPB Leipzig
Leipzig, Germany
https://jobs.zeit.de/jobs/researcher-postdoc-cheminformatics-m-f-d-leibniz-institut-fuer-pflanzenbiochemie-ipb-halle-saale-1087235
Research Associate in AI for Chemistry
Imperial College London
London, UK
https://www.jobs.ac.uk/job/DHJ529/research-associate-in-ai-for-chemistry
PhD Student in ‘Digital Chemistry’
Wuppertal University
Wuppertal, Germany
https://fsk-lab.github.io/news/24-04-10-hiring
Cheminformatics…
ELN (Electronic Lab Notebook) Finder
https://eln-finder.ulb.tu-darmstadt.de/home
“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
https://pubs.acs.org/doi/10.1021/acs.jcim.4c00049
… so don’t just plug everything together to ‘make it bigger’
FragGrow
http://fraggrow.xundrug.cn
‘FragGrow is a web server for structure-based drug design by fragment growing’
Faerun
https://pypi.org/project/faerun/0.1.28
‘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
https://youtu.be/w1rDxAtSb_w
PlayMolecule Viewer: A Toolkit for the Visualization of Molecules and Other Data
https://pubs.acs.org/doi/10.1021/acs.jcim.3c01776
‘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
https://pubs.acs.org/doi/10.1021/acs.jcim.3c01406
‘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’
euroSAMPL
https://qmbench.net/eurosampl
‘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
https://www.sciencedirect.com/science/article/pii/S0092867424000059
… 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
https://onlinelibrary.wiley.com/doi/10.1002/ail2.91
https://github.com/O-Schilter/Clipboard-to-SMILES-Converter
(Oliver is also presenting in the Cheminformatics Meeting next week, please see above)
AiZynth impact on medicinal chemistry practice at AstraZeneca
https://pubs.rsc.org/en/content/articlelanding/2024/md/d3md00651d
Predicting synthesis – and examples of impact
Will the real INS018_055 please stand up?
https://cdsouthan.blogspot.com/2024/03/will-real-ins018055-please-stand-up.html
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
https://jump-cellpainting.broadinstitute.org
It’s Been a Decade of AI in the Drug Discovery Race. What’s Next?
https://www.biopharmatrend.com/ai-drug-discovery-pipeline
Review of the pipelines of some of the larger AI-driven drug discovery companies
Patterns in Practice
https://lifeofdata.org/site/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
https://www.nature.com/articles/s41698-024-00553-6
Florian Markowetz on the difference between theory in practice, in the clinical prediction context
HitchhikersAI
https://www.hitchhikersai.org
‘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?’
https://drive.google.com/file/d/1NaG8b54SnwFp3OiVpNbTBgSRBs0zx54L/view
Presentation by Derek Lowe on the above topic
Dense grid searches over neural network hyperparameters…
https://twitter.com/jaschasd/status/1756930242965606582
… look like the beauty, but they are the beast
Quality criteria for degraders – Probing biology with a novel modality
https://www.youtube.com/watch?v=w1Ky6NjmmRI
Presentation by Ingo Hartung
Evaluation of clinical prediction models (part 1): from development to external validation
https://www.bmj.com/content/384/bmj-2023-074819.full
… 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
https://www.pnas.org/doi/10.1073/pnas.1609793113
Very true… and even since 2016 we have probably moved further into this direction
Scientists turn to AI to make beer taste even better
https://www.theguardian.com/technology/2024/mar/26/ai-beer-taste-better-belgium-scientists
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
https://futurism.com/microsoft-copilot-alter-egos
… but who doesn’t want to have a ‘godlike AGI’ anyway!
AI applied to the illustration of scientific articles
https://twitter.com/MadS100tist/status/1758128836523548858
… 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
https://arxiv.org/html/2404.01833v1
… another way to ‘break’ LLMs
A moment that changed me: I patronised a refugee – and he taught me an invaluable lesson
https://www.theguardian.com/lifeandstyle/2024/feb/28/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’
https://www.theguardian.com/world/2024/mar/25/sagrada-familia-barcelona-completed-2026-stairway
I find this idea honestly _very_ strange
Match Group and Managed Dissatisfaction
https://www.thediff.co/archive/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
https://www.theguardian.com/lifeandstyle/2024/mar/10/how-an-epic-climb-lifted-one-woman-out-of-lifes-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,
Andreas