Dear All,
I would like to circulate some current Cheminformatics- (and related) news to everyone as follows. If you have information from your side for distribution please just let me know, and I am happy to include it on the next occasion.
So here we go…
Events
1/2 September 2022
5th RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry
Cambridge, UK
https://www.rsc.org/events/detail/73047/5th-rsc-bmcs-rsc-cicag-artificial-intelligence-in-chemistry
2/3 September 2022
1st International Conference on Drug Repurposing
Maastricht, The Netherlands
https://repo4.eu/rexpo22-conference/
7 September 2022
Cambridge Cheminformatics Meeting
Hybrid Cambridge, UK/Online
http://c-inf.net/
18-21 September 2022
16th International Congress of Toxicology
Maastricht, The Netherlands
https://www.ict2022.com/
18/19 October 2022
Bio-IT World Europe
Berlin, Germany
https://www.bio-itworldeurope.com/
Jobs
Molecular Data Sciences – Principal Scientist
Sanofi
Vitry-sur-Seine, France
https://www.linkedin.com/jobs/view/3061312900
VP Modelling and Informatics, Senior Scientist Computational Chemistry, and Others
Charm Therapeutics
Cambridge and London, UK
https://charmtx.com/jobs/
Scientist – Data, QSAR Models and Adverse Outcome Pathways
Lhasa Limited
Leeds, UK
https://www.lhasalimited.org/vacancies/scientist/10004
Cheminformaticians, Computational Chemists, Computational Systems Biologist, and others
Healx
Remote/Cambridge, UK
https://boards.greenhouse.io/healx
Postdoctoral fellowship in computational drug design
University of Antwerp
Antwerp, Belgium
https://www.linkedin.com/jobs/view/3141583774
Cheminformatics & Drug Design Scientist
Bellvitge Biomedical Research Institute – IDIBELL
Barcelona, Spain
https://www.linkedin.com/jobs/view/3139738257
Senior/Principal Scientist, Structural Biology
Ambagon Therapeutics
Eindhoven, The Netherlands
https://www.linkedin.com/jobs/view/3070801938
Molecular Modeler
Nostrum Biodiscovery
Barcelona, Spain
https://www.linkedin.com/comm/jobs/view/3134910348
Computational Chemist/PostDoc Machine Learning for Chemical Synthesis Planning
Bayer
Berlin, Germany
https://karriere.bayer.de/en/job/computational-chemist–postdoc-machine-learning-for-chemical-synthesis-planning-m-f-d–SF642068_en_US
Cheminformatics Scientist
GSK
Stevenage, UK
https://gsk.wd5.myworkdayjobs.com/GSKCareers/job/UK—Hertfordshire—Stevenage/Cheminformatics-Scientist_336642-1
Senior Research Associate – Machine Learning, Molecular Modeller
Astex
Cambridge, UK
https://www.cloudonlinerecruitment.co.uk/Astex/VacancyDetails.aspx?FromSearch=True&MenuID=&VacancyID=16
https://www.cloudonlinerecruitment.co.uk/Astex/VacancyDetails.aspx?FromSearch=True&MenuID=&VacancyID=17
Cheminformatics Data Scientist, Discovery Science Team Leader, Research and Applications Scientists, and Others
Cambridge Crystallographic Data Centre
Cambridge, UK
https://www.ccdc.cam.ac.uk/theccdcprofile/careers/
Senior Scientific Developer
AstraZeneca
Royston, UK
https://careers.astrazeneca.com/job/royston/senior-scientific-developer/7684/29878761760
Cheminformatics…
VSFlow: an open-source ligand-based virtual screening tool
https://chemrxiv.org/engage/chemrxiv/article-details/628c60215d9485a206cc8ecc
https://github.com/czodrowskilab/VSFlow/wiki
By Paul Czodrowski and colleagues, based largely on RDKit
StarGazer: A Hybrid Intelligence Platform for Drug Target Prioritization and Digital Drug Repositioning Using Streamlit
https://www.frontiersin.org/articles/10.3389/fgene.2022.868015/full
https://github.com/AstraZeneca/StarGazer
Courtesy of AstraZeneca
Cambridge Cheminformatics Meeting, 8 June – Slides and Recording now Available
http://c-inf.net/
On efficient fingerprints, graphs, and free energy calculations
Chemfp 4.0 is out
https://chemfp.readthedocs.io/en/latest/whatsnew.html
Chemfp is an analytics package for cheminformatics fingerprints. It contains command-line tools and an extensive Python library for fingerprint generation, high-performance similarity search, diversity selection, and exploratory research.
Evaluation guidelines for machine learning tools in the chemical sciences
https://www.nature.com/articles/s41570-022-00391-9
A review we recently co-authored to strive towards better assessment of AI/ML models in the chemical field
On the Frustration to Predict Binding Affinities from Protein–Ligand Structures with Deep Neural Networks
https://pubs.acs.org/doi/full/10.1021/acs.jmedchem.2c00487
It should work better… but does it, really? An insightful paper by Didier Rognan and colleagues
Drug Structures, MedChem Structures Genius
https://apps.apple.com/us/app/drug-structures/id1207401347
https://play.google.com/store/apps/details?id=fr.univ.lille2&hl=gsw&gl=US
If you have a few minutes… the best way to make a chemist happy is of course to look at some structures
AI in Drug Discovery Podcast
https://podcasts.apple.com/us/podcast/ai-how-to-think-differently/id1589989419?i=1000566339894
A recent podcast, by The Technology Partnership (TTP); with Sarah Morrow, Aaron Morris, and Andreas Bender
…beyond Cheminformatics…
OpenFold
https://github.com/aqlaboratory/openfold
https://openfold.io/
A faithful but trainable PyTorch reproduction of DeepMind’s AlphaFold 2
The open database for university spinouts
https://www.spinout.fyi
Which terms did you get for your spin-out? Sharing data to improve upon the current state of affairs
Artificial Intelligence Meets Natural Stupidity
https://cs.fit.edu/~kgallagher/Schtick/Serious/McDermott.AI.MeetsNaturalStupidity.pdf
An article from 1976. Did things really move on since then though?
A model for learning strings is not a model of language
https://www.pnas.org/doi/10.1073/pnas.2201651119
My algorithm is alive! (Or is it?)
Artificial intelligence is breaking patent law
https://www.nature.com/articles/d41586-022-01391-x
The computer as an inventor – suggestions to development patent law further
Is MDPI a predatory publisher?
https://paolocrosetto.wordpress.com/2021/04/12/is-mdpi-a-predatory-publisher/
Publishing – where should I?
The ASA Statement on p-Values: Context, Process, and Purpose
https://www.tandfonline.com/doi/full/10.1080/00031305.2016.1154108
Possibly read before but… likely worth a read again (and again)
It escaped me before, but … also TikTok are now entering AI for drug discovery
https://techcrunch.com/2020/12/23/bytedance-ai-drug/
Tik tok tik… and here it is!
… and clearly beyond cheminformatics
“Jeff Dean spent enough money to feed a family of four for half a decade to get a 0.03% improvement on CIFAR-10.”
https://www.reddit.com/r/MachineLearning/comments/uyratt/d_i_dont_really_trust_papers_out_of_top_labs/
Discussion on Reddit about ML models, their performance and performance improvements, put into real-world context
UN Warns of ‘Total Societal Collapse’ Due to Breaching of Planetary Boundaries
https://bylinetimes.com/2022/05/26/un-warns-of-total-societal-collapse-due-to-breaching-of-planetary-boundaries/
So what will ‘The AI'(TM) do about it?
The man who built his own cathedral
https://www.theguardian.com/world/2022/may/31/the-man-who-built-his-own-cathedral-justo-gallego-mejorada-del-campo-spain
What drives him? (And what drives you? And me?)
A New Explanation for the Mystery of Rasputin’s Survival of Cyanide Poisoning: Eating Raw Garlic
https://pubs.acs.org/doi/10.1021/acs.chemrestox.2c00187
I can entirely relate to that – before I went to India the first time for a few months I ate lots of raw onions, ‘just to prepare myself’
They’re Made out of Meat
https://www.mit.edu/people/dpolicar/writing/prose/text/thinkingMeat.html
Me (and you?) too
Rasta Love Feat. Ky-Mani Marley, Protoje/The Seven Year Itch
https://music.youtube.com/watch?v=0bctXoFpO3c&list=RDTMAK5uy_kset8DisdE7LSD4TNjEVvrKRTmG7a56sY
Really good. (OK, that’s a bit boring. But basically – it’s just really, really good.)
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 or Digital Science for Drug Discovery Meetings, please just let me know, cheers!
Best wishes,
Andreas