Cambridge Cheminformatics Newsletter – Christmas 2023 Edition

Dear All,

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

In particular, please note the Cambridge Cheminformatics Meeting on 6 December (Wednesday this week) – in person at the CCDC, and on Zoom, so everyone can attend as desired.

And here we go…

Events

5 December 2023
MedChemCASES #30 – Magnus Nilsson
Discovery of the Potent and Selective Inhaled Janus Kinase 1 Inhibitor AZD4604 and Its Preclinical Characterization
https://us06web.zoom.us/webinar/register/WN_NuIfQ3jFR42tbo3ZW3vlWA

6 December 2023
Cambridge Cheminformatics Meeting
Cambridge, UK and on Zoom (Hybrid)

More information: http://www.c-inf.net
Direct Zoom registration:  https://cam-ac-uk.zoom.us/meeting/register/tZcpdeysqjIqGtXy-J4Ul09RqNOMiuvF-odf

Programme

Assessing Conformations of Small Molecules Against the Cambridge Structural Database
Patrick McCabe, Cambridge Crystallographic Data Centre
https://www.ccdc.cam.ac.uk

SILVR: Guided Diffusion for Molecule Generation
Nicholas Runcie, University of Edinburgh / currently AstraZeneca
https://mey-research.org/team

From Data Mangling to Data Wrangling
Donald Daley, Androit DI
http://adroitdi.com

11 January 2024
AIBIO-UK Kick-Off Meeting
Birmingham, UK and on Zoom (Hybrid)
https://aibio.ac.uk

18 January 2024
6th International Mini-Symposium on Molecular Machine Learning (MML)
Virtual Event
https://www.uni-muenster.de/SPP2363/Meetings/meetings.html

29 January – 2 February 2024
7th Advanced in silico Drug Design Workshop/Challenge 2024
Olomouc, Czech Republic/Lectures Hybrid
https://www.kfc.upol.cz/7add

13-15 May 2024
2024 Workshop on Free Energy Methods in Drug Design
Leiden, The Netherlands
http://alchemistry.org/wiki/2024_Workshop_on_Free_Energy_Methods_in_Drug_Design

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

1-3 July 2024
Joint CCPBioSim & MGMS Annual Conference
Newcastle, UK
https://ccpbiosim.ac.uk/events/upcoming-events/eventdetail/114/18,19,20/ccpbiosim-annual-conference

2-4 July 2024
7th Machine Learning and AI in Bio(Chemical) Engineering Conference
Cambridge, UK
https://www.mabc-cambridge.ai

11-13 September 2024 (save the date!)
RDKit UGM 2024
Zurich, Switzerland
https://github.com/rdkit

3-6 November 2024
18th German Conference on Cheminformatics
Bad Soden am Taunus, Germany
https://veranstaltungen.gdch.de/tms/frontend/index.cfm?l=11576

Jobs

Experienced Computational Chemist
Pharmaron
Hoddesdon, UK
https://www.linkedin.com/jobs/view/3762941732

Professorship for Artificial Intelligence for the Molecular Sciences
University of Wuerzburg
Wuerzburg, Germany
https://www.uni-wuerzburg.de/fileadmin/43150000/2023/Ausschreibungen/2023_AI4MS_Ausschreibung_en_publish.pdf

Postdoctoral Fellow – Deep-Learning In Early Drug Discovery
Merck
Darmstadt, Germany
https://www.linkedin.com/jobs/view/3760110913

Full Professor of Computational Material Discovery
University of Vienna
Vienna, Austria
https://personalwesen.univie.ac.at/jobs-recruiting/professuren/detail-seite/news/computational-material-discovery-1

Chemoinformatician / Bioinformatician
Purposeful
Athens, Greece
https://www.linkedin.com/jobs/view/3774382499

Scientist, Predictive Molecular Research
BMS
Seville, Spain
https://www.linkedin.com/jobs/view/3761422671

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

Cheminformatician
SoseiHeptares
Cambridge, UK
https://cezanneondemand.intervieweb.it/heptares/jobs/cheminformatician-computational-chemistry-team-37704/en

Research Associate in Computational Chemistry
https://www.bath.ac.uk/jobs/Vacancy.aspx?ref=ED11204
Bath University
Bath, UK

Postdoctoral Researcher Chemoinformatics
Palacky University
Olomouc, Czech Republic
https://www.linkedin.com/jobs/view/3772977453

AI/Cheminformatics Intern
Pangea Bio
Berlin, Germany
https://www.linkedin.com/jobs/view/3765822237

PhD Position: Digital Twins for Ecotoxicology: Leveraging Artificial Intelligence and Multi-Omics for Chemical Risk Assessment
University of Birmingham
Birmingham, UK
https://warwick.ac.uk/fac/cross_fac/mibtp/phd/sustainable_agriculture_and_food/ecotoxicology

Cheminformatics…

“datamol.io is an open-source toolkit that simplifies molecular processing and featurization workflows for ML scientists in drug discovery”
https://datamol.io
E.g. the MedChem filters might be particularly useful: https://github.com/datamol-io/medchem

FPSim2
https://chembl.github.io/FPSim2/index.html
“FPSim2 is a small NumPy centric Python/C++ package to run fast compound similarity searches”

Real-World Molecular Out-Of-Distribution: Specification and Investigation
https://chemrxiv.org/engage/chemrxiv/article-details/64c012a1b053dad33ae21932
What is ‘distribution’ in molecular space anyway? What’s inside, what’s outside; what is interpolation, what extrapolation?

DrugOOD: Out-of-Distribution (OOD) Dataset Curator and Benchmark for AI-aided Drug Discovery
https://arxiv.org/pdf/2201.09637.pdf
Related to the previous item. May all of this improve practical decision making in the future

REINVENT4
https://github.com/MolecularAI/REINVENT4
REINVENT reinvented  

“Exploring Python-Wrapped Docking Tools: A Comparative Analysis”
https://www.linkedin.com/posts/adrian-jasinski-phd_comparison-of-python-wrappers-for-molecular-ugcPost-7134914621278154752-QpNy

On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00781-1
Who validates gets numbers, for sure… but are those numbers actually valid?

Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15
https://www.nature.com/articles/s42004-023-00991-6
Everyone just wants to fold proteins these days

DataPype: A Fully Automated Unified Software Platform for Computer-Aided Drug Design
https://pubmed.ncbi.nlm.nih.gov/37901539
As it says on the tin

Adapting to the Changing Landscape of Biotech-Driven Drug Discovery
https://pubs.acs.org/doi/10.1021/acs.jmedchem.3c02035
Excellent article by Dean Brown – and I absolutely agree; we will also start ‘Fireside Chats’ in the Cambridge Cheminformatics Meetings shortly, so stay tuned!

… beyond cheminformatics …

CIPSI – Chemical Intellectual Property Service @ IMIM
https://cipsi.org/
Quite a neat interface for chemical patent searching

Extracting Training Data from ChatGPT
https://not-just-memorization.github.io/extracting-training-data-from-chatgpt.html
… some have seen it coming!

A researcher who publishes a study every two days reveals the darker side of science
https://english.elpais.com/science-tech/2023-06-04/a-researcher-who-publishes-a-study-every-two-days-reveals-the-darker-side-of-science.html
This hole is rather deep…

The strain on scientific publishing
https://arxiv.org/ftp/arxiv/papers/2309/2309.15884.pdf
Quantity is not quality; and … choose a ‘proper journal’, I tell you!

Two Decades of Online Teaching: Trends, Challenges, and Future Directions
https://www.chimia.ch/chimia/article/view/2023_683
(related to chemistry)

“Why Nature Portfolio should have never published the Google AI for Materials article”
https://www.linkedin.com/posts/ongsp_a-google-ai-has-discovered-22m-materials-activity-7136223630731988992-hHlZ

“This exciting paper shows AI design of materials, robotic synthesis. 10s of new compounds in 17 days. But did they?”
https://twitter.com/Robert_Palgrave/status/1730358675523424344
… Honestly, Nature et al. have become a bit of a joke these days

… and clearly beyond cheminformatics

Nature’s perfection…
https://www.linkedin.com/feed/update/urn:li:activity:7126809106690043904

… and Nature’s freakshow
https://www.linkedin.com/posts/dennis-koester-80260b88_what-is-so-special-about-this-molecule-activity-7134315468483432448-NcXd

A posthumous honor for the man who saved the world
https://thebulletin.org/2018/09/a-posthumous-honor-for-the-man-who-saved-the-world/
Honestly: Thank you, Stanislav!

Too much stuff: can we solve our addiction to consumerism?
https://www.theguardian.com/environment/2023/nov/28/too-much-stuff-can-we-solve-our-addiction-to-consumerism
… just in time for Christmas!

Archaeologists reveal life stories of hundreds of people from medieval Cambridge
https://www.theguardian.com/science/2023/dec/01/archaeologists-life-stories-medieval-cambridge
https://www.aftertheplague.org

‘I left the cinema, walked home and announced I was moving’: films that made people emigrate
https://www.theguardian.com/film/2023/dec/02/i-left-the-cinema-walked-home-and-announced-i-was-moving-films-that-made-people-emigrate
Pretty energetic ways to make decisions in their lives – well done everyone!

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.

Have a good Christmas and start into the New Year everyone, see you again shortly!

Best wishes,

Andreas