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Cambridge Cheminformatics Newsletter, January/February 2024 Edition

Dear All,

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

In particular, I would like to point out the first EFMC2 Tandem Talk this year, which will take place on 15 February virtually, and the first Cambridge Cheminformatics Meeting, which will take place on 21 February in hybrid mode; for further information please see below.

The dates for the Cambridge Cheminformatics Meetings in 2024 are now also fixed – after 21 February this will be 8 May, 4 September and 13 November. Please mark your calendar, more information will be circulated before each meeting via this newsletter.

So here we go…

Events

15 February 2024
EFMC2 Tandem Talk
Virtual Event
“BAY-069, a Novel (Trifluoromethyl)pyrimidinedione-Based BCAT1/2 Inhibitor and Chemical Probe”
https://www.efmctandemtalks.org

21 February 2024
Cambridge Cheminformatics Meeting
Hybrid – at CCDC, Cambridge and on Zoom
More Information (and all 2024 dates): http://www.c-inf.net
Zoom registration: https://cam-ac-uk.zoom.us/meeting/register/tZEucuqvpjMoHdBZaZFY8oHvSKQU623zJJft

Programme:

MolFlux: A Python Ecosystem for Molecular Machine Learning
Ward Haddadin, ExScientia
https://www.linkedin.com/in/ward-haddadin-1600092a

Ten Years of Extracting Reactions: Where Did We Come From, Where Do We Go?
John Mayfield, NextMove
https://www.linkedin.com/in/johnwmay

Practical Machine Learning for Synthetic Chemistry
Emma King-Smith, University of Cambridge
https://www.wolfson.cam.ac.uk/people/dr-emma-king-smith

Please join us and circulate further!

26 February 2024
NFDI4 Chem Community Workshop
Mainz, Germany
https://www.nfdi4chem.de/event/nfdi4chem-community-workshop

1 March 2024
NextGen Basel 1 – Next Generation Product Design and Risk Assessment
Basel, Switzerland and Virtual (Hybrid)
https://saferworldbydesign.com/nextgen-basel-1

3-5 March 2024
9th Fragment-based Drug Discovery Meeting
Hinxton Hall/near Cambridge, UK
https://www.rscbmcs.org/events/fragments24

4-6 March 2024
International Leopoldina Symposium on Molecular Machine Learning
Halle, Germany
https://indico.uni-muenster.de/event/2377

11 April 2024
UK QSAR Meeting
Babraham Research Campus, Cambridge, UK
https://ukqsar.org/index.php/2024/01/22/uk-qsar-spring-2024-meeting

13-17 May 2024
Bolzano, Italy
International Workshop on Open Molecular Informatics (IWOMI)
https://www.iwomi.net

19-23 May 2024
European Workshop in Drug Design
Siena, Italy
https://ewdd24.org

24-28 June 2024
Strasbourg Summer School in Chemoinformatics 2024
Strasbourg, France
https://infochim.chimie.unistra.fr/?p=973

2 July 2024
Milner Therapeutics Symposium 2024
Cambridge, UK
https://www.milner.cam.ac.uk/milner-therapeutics-symposium-2024

8-11 September 2024
Eurotox
Copenhagen, Denmark
https://www.eurotox2024.com

Jobs

Assistant Professor in Computational Chemistry / Data Science
Durham University
Durham, UK
https://durham.taleo.net/careersection/du_ext/jobdetail.ftl?job=23002225

Principal Scientist – CADD
Novartis
Emeryville, CA
https://www.novartis.com/careers/career-search/job-details/388177br/principal-scientist-cadd

Chemoinformatics Data Scientist
Bayer
Frankfurt, Germany
https://www.linkedin.com/jobs/view/3774638152

Postdoc – Virtual screening and molecular dynamics simulations in early stage drug development
University of Oslo
Oslo, Norway
https://www.uio.no/dscience/english/dstrain/research-areas/pharmacy/computer-aided-drug-design

Postdoctoral Scientist – Structural Studies
MRC Laboratory of Molecular Biology
Cambridge, UK
https://www.jobs.ac.uk/job/DFL014/postdoctoral-scientist-structural-studies-dr-joe-greener-lmb-2331

PhD Studentships – AI in Drug Discovery
Queen Mary University of London
London, UK
https://www.qmul.ac.uk/deri/ukri-aidd-doctoral-training-programme

Internship on Cheminformatics
Covestro
Leverkusen, Germany
https://www.linkedin.com/jobs/view/3805342646

AI/Cheminformatics Intern
Pangea Bio
Berlin, Germany
https://www.linkedin.com/jobs/view/3802737066

Cheminformatics…

Scipion-Chem: An Open Platform for Virtual Drug Screening
https://pubs.acs.org/doi/10.1021/acs.jcim.3c01085
Plug-in based and with GUI, see also https://github.com/scipion-chem

AI-driven molecular generation of not-patented pharmaceutical compounds using world open patent data
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00791-z
… not everything the computer comes up with is what you really want to make

“MolFlux is a foundational package for molecular predictive modelling. From data to features to models, MolFlux provides you with a complete ecosystem for building and handling machine learning models!”
https://exscientia.github.io/molflux
Also see https://exscientia.github.io/physicsml

httk: High-Throughput Toxicokinetics
https://cran.r-project.org/web/packages/httk/index.html
… it’s not all about fancy AI, always make sure you consider PK!

Some Thoughts on Biotech vs Pharma for Computational Chemists
http://practicalcheminformatics.blogspot.com/2023/12/some-thoughts-on-biotech-vs-pharma-for.html
Excellent blog post by Dean Brown

SMARTS+
https://smarts.plus
“Create an easy to comprehend visualization for your SMARTS expression. While our Compare, Search and Create functionality is limited to SMARTS, the viewer is handling Reaction SMILES, Reaction SMARTS and SMIRKS as well.”

QPTUNA
https://github.com/MolecularAI/Qptuna
“Build predictive models for CompChem with hyper-parameters optimized by Optuna.”

Scikit-Mol – Easy Embedding of RDKit into Scikit-Learn
https://www.cheminformania.com/scikit-mol-easy-embedding-of-rdkit-into-scikit-learn
On the integration of two toolkits many of us use

GUIDEMOL: A Python graphical user interface for molecular descriptors based on RDKit
https://onlinelibrary.wiley.com/doi/10.1002/minf.202300190
… making RDKit more accessible via GUI

Cambridge Cheminformatics Meeting Recording from 6 December 2023 now Online
https://www.youtube.com/watch?v=qTi-OA8bs6g
… on assessing conformations against the CSD, guided diffusion for molecular generation, and handling drug discovery data

Digidrug Recording from 29 November 2023 now Online
https://youtu.be/hNPYAQjA6Tc
… on ML for drug discovery with low data, and fast QM quality strain energy with neural network potentials

DataWarrior… probably widely known, but circulated again due to lots of new features in recent versions
https://openmolecules.org/datawarrior
… such as docking, patent search, retrosynthesis, building block search, etc.

Vina-GPU 2.1: towards further optimizing docking speed and precision of AutoDock Vina and its derivatives
https://www.biorxiv.org/content/10.1101/2023.11.04.565429v1
First there was AutoDock, then AutoDock Vina, then Vina-GPU…

ADMET-AI: A machine learning ADMET platform for evaluation of large-scale chemical libraries
https://www.biorxiv.org/content/10.1101/2023.12.28.573531v1
https://admet.ai.greenstonebio.com

PKSmart: An Open-Source Computational Model to Predict in vivo Pharmacokinetics of Small Molecules
https://www.biorxiv.org/lookup/content/full/2024.02.02.578658v1
https://pk-predictor.serve.scilifelab.se
“PKSmart is an open-source app framework built specifically for predicting human and animal PK parameters.”

RSC CICAG Newsletter – Winter 2023/24
https://www.rsccicag.org/index_htm_files/CICAG%20Newsletter%20Winter%202023-24%20FINAL.pdf
Lots of news from RSC CICAG

… beyond Cheminformatics …

“PostgresML is a complete MLOps platform in a PostgreSQL extension. Build simpler, faster and more scalable models right inside your database.”
https://postgresml.org

“Friends Don’t Let Friends Make Bad Graphs”
https://github.com/cxli233/FriendsDontLetFriends
Yup

“The pharma industry from Paul Janssen to today: why drugs got harder to develop and what we can do about it”
https://atelfo.github.io/2023/12/23/biopharma-from-janssen-to-today.html
Beautifully written, also with interesting facts and historic pictures

“The rise and fall of the industrial R&D lab”
https://worksinprogress.co/issue/the-rise-and-fall-of-the-american-rd-lab
Once it was Bell and AT&T, now Google and Microsoft… but why do they actually do it?

Atlas Venture 2023 Year in Review
https://www.youtube.com/watch?v=0DIgT32bFV4
by Bruce Booth

“Who´s to blame for octanol”
https://mcconnellsmedchem.com/2024/01/08/lipophilicity/
Sometimes it’s an event deep down in history that influences what is still being done today

“New analysis raises doubts over autonomous lab’s materials ‘discoveries’”
https://www.chemistryworld.com/news/new-analysis-raises-doubts-over-autonomous-labs-materials-discoveries/4018791.article
Damn… but wasn’t it published in … Nature?!

AlphaGeometry
https://www.linkedin.com/feed/update/urn:li:activity:7154157779136446464
Yep, here we go again

“More Is Different”
https://www.tkm.kit.edu/downloads/TKM1_2011_more_is_different_PWA.pdf
Broken symmetry and the nature of the hierarchical structure of science

… and clearly beyond cheminformatics

Reminiscences from the End of the Horse Era in New York City

https://untappedcities.com/2022/02/21/horse-era-new-york-city

A truly unique city in the good ol’ times

Possibly of current interest
https://www.scientificamerican.com/article/the-shared-psychosis-of-donald-trump-and-his-loyalists
https://www.dcreport.org/2021/01/05/the-georgia-phone-call-who-needs-a-psychiatric-examination
“The relationship between Trump and his supporters is an abusive one, as an author of the 2017 book I edited, The Dangerous Case of Donald Trump, presciently pointed out. When the mind is hijacked for the benefit of the abuser, it becomes no longer a matter of presenting facts or appealing to logic.”

Bogosort
https://en.wikipedia.org/wiki/Bogosort
A crucial algorithmic breakthrough I missed until now! Also check out ‘related algorithms’ section

View from inside Google
https://www.linkedin.com/feed/update/urn:li:activity:7153269568893775872
“My hot take: Google does not have one single visionary leader. Not a one. From the C-suite to the SVPs to the VPs, they are all profoundly boring and glassy-eyed.”

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

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