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Cambridge Cheminformatics Newsletter, 13 December 2022

Dear All,

A last newsletter for 2022 with some current Cheminformatics- (and related) news I would like to circulate to everyone in these turbulent times! 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.

I wish everyone a peaceful holiday period/Christmas time and all the best for 2023!

So here we go…

Events

12 January 2023
Discngine Labs: Protein structure prediction – What’s next after AlphaFold?
Virtual Event
https://www.discngine.com/event/2023/01/1/discngine-labs-protein-structure-prediction

19 January 2023
5th International Mini-Symposium Molecular Machine Learning
Virtual Event
https://www.uni-muenster.de/Chemie.oc/glorius/symposium_mml.html

19-21 June 2023
Ninth Joint Sheffield Conference on Chemoinformatics – Call for Papers is out!
Sheffield, UK
https://cisrg.shef.ac.uk/shef2023/

Cambridge Cheminformatics Meetings – dates for 2023 have been set
http://www.c-inf.net

Vacancies

Molecular Modeller
Orion
Espo or Turku, Finland
https://www.orion.fi/en/careers/open-vacancies?rmpage=job&rmjob=1753&rmlang=UK

Senior CADD Scientist
PharmEnable
Remote First / Cambridge, UK
https://pharmenable.com/careers/senior-cadd-scientist/

Lecturer in Digital Chemistry
University of York
York, UK
https://www.jobs.ac.uk/job/CVG697/lecturer-in-digital-chemistry-teaching-and-scholarship

Staff Scientist in Cheminformatics & Drug Design, Computational Lab Manager
IDIBELL
Barcelona, Spain
https://jobs.idibell.cat/jobs/1865679-staff-scientist-in-cheminformatics-drug-design-computational-lab-manager

Director/Senior Director, Computational Design
Treeline Biosciences
Watertown, MA
https://www.linkedin.com/jobs/view/3357674425

Quantum Computing Scientist
Boehringer Ingelheim
Ingelheim, Germany
https://www.linkedin.com/jobs/view/3354454541

Computational Surface Chemist
ASML
Veldhoven, The Netherlands
https://www.linkedin.com/jobs/view/3263170936

Principal Scientist, Cheminformatics
Pfizer
Berlin, Germany
https://www.linkedin.com/jobs/view/3326547143

Senior Computational Biologist
Merck
Shanghai, China
https://www.linkedin.com/jobs/view/3366905133

Postdoctoral Position in Molecular Modelling and Machine Learning
INSERM
Paris, France
https://www.linkedin.com/posts/maria-miteva-62180510_postdoctorate-offer-activity-7000459379724460032-3g4H

Computational Chemist
Pharmacelera
Barcelona, Spain
https://www.linkedin.com/feed/update/urn:li:activity:7000746014596829184/

Senior and Principal Scientist, Computational Chemistry
Charm Therapeutics
Remote / Cambridge, UK
https://www.linkedin.com/jobs/view/3364830540
https://charmtx.com/careers/principal-scientist-computational-chemist/?gh_jid=4104615101

Professor for Artificial Intelligence in Chemistry and Chemical Biology
University of Dortmund
Dortmund, Germany
https://www.academics.de/jobs/universitaetsprofessur-w2-artificial-intelligence-in-chemistry-and-chemical-biology-technische-universitaet-dortmund-dortmund-1068127

Computational Toxicologist
GSK
Stevenage, UK
https://gsk.wd5.myworkdayjobs.com/GSKCareers/job/UK—Hertfordshire—Stevenage/Computational-Toxicologist_353567-1

PhD Positions – Reactivity Prediction and Design, Neural ODEs, Pollutants in Aquatic Life
Bath University
Bath, UK
https://www.findaphd.com/phds/project/epsrc-dtp-phd-project-machine-learning-and-reaction-modelling-a-synergistic-approach-to-rapid-reactivity-prediction/?p150280
https://www.findaphd.com/phds/project/big-data-and-machine-learning-for-reaction-design/?p150466
https://www.findaphd.com/phds/project/transparency-in-neural-ordinary-differential-equations/?p127115
https://www.findaphd.com/phds/project/nerc-gw4-dtp-phd-project-understanding-the-impact-of-pollutants-on-aquatic-life-machine-learning-synthesis-and-transport-mechanisms/?p148369

Cheminformatics…

LinChemIn: SynGraph. A data model and a toolkit to analyze and compare synthetic routes
https://chemrxiv.org/engage/chemrxiv/article-details/6376222e53ab80ebb2290281

Fragmenstein: Scaffold hopping between bound compounds by stitching them together like a reanimated corpse
https://github.com/matteoferla/Fragmenstein

Mining Ring Systems in Molecules for Fun and Profit
https://practicalcheminformatics.blogspot.com/2022/12/identifying-ring-systems-in-molecules.html
Blog post by Pat Walters

Calibration and generalizability of probabilistic models on low-data chemical datasets with DIONYSUS
https://arxiv.org/abs/2212.01574

Dimorphite-DL – protonate compounds at specified pH
https://durrantlab.pitt.edu/dimorphite-dl/
Not many other open source solutions around!

Cross-Site Cambridge/Oxford/Berlin Digital Drug Discovery and Cheminformatics Meeting, 30 November
https://youtu.be/zA3sktlzl08
Video Online (on Searching Ultra-Large Chemical Libraries; and Fragmenstein/Fragment-Based Drug Discovery)

BTS In Silico/Mechanistic Toxicology Workshop: Hands-on Modelling of Safety Data for Non-Experts – recording online
https://youtu.be/a4Mv61FjRjc
Seminar of the British Toxicology Society, aiming to bring toxicologists and computational modellers closer together for mutual benefit

… beyond Cheminformatics…

Machine Learning: The Great Stagnation
https://towardsdatascience.com/machine-learning-the-great-stagnation-3a0f044e17e0
“Machine Learning PhD students are the new Investment Banking analysts, both seek optionality in their career choices but differ in superficial ways like preferring Meditation over Parties and Marijuana & Adderall over Alcohol and Cocaine.” Discuss!

VeLO, the first hyperparameter-free learned optimizer that outperforms hand-designed optimizers on real-world problems
https://twitter.com/jmes_harrison/status/1593422054971174912
The optimal optimizer then?

How to avoid machine learning pitfalls: a guide for academic researchers
https://arxiv.org/pdf/2108.02497.pdf
For chemistry-specific aspects also see: http://www.drugdiscovery.net/howToLie

Writing a scientific article: A step-by-step guide for beginners
https://www.sciencedirect.com/science/article/pii/S1878764915001606

How complex systems fail
https://www.researchgate.net/publication/228797158_How_complex_systems_fail
Quite universally applicable

EFMC Series on Hit Generation
https://www.efmc.info/hit-generation
Covers different readout types, fragment-based design, DELs, etc.

Valuation and Returns of Drug Development Companies: Lessons for Bioentrepreneurs and Investors
https://link.springer.com/article/10.1007/s43441-021-00364-y

Publication-ready NN-architecture schematics
https://github.com/alexlenail/NN-SVG

Biopharmaceutical R&D outsourcing: Short-term gain for long-term pain?
https://www.sciencedirect.com/science/article/pii/S1359644622003038
Bit theoretical, but still valid in many aspects

High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations
https://www.nature.com/articles/s41592-022-01667-0

Broad Institute Machine Learning in Drug Discovery (MLinDD) Symposium 2022
https://www.youtube.com/playlist?list=PLlMMtlgw6qNh-MH4-dsl0griJ-Bh1dtWJ
Videos online

IFITM proteins assist cellular uptake of diverse linked chemotypes
https://www.science.org/doi/10.1126/science.abl5829
How come your bitopic inhibitor works in vivo? Thank the IFITMs!

… and certainly beyond Cheminformatics

Molnupiravir is a very effective anti-Covid drug…
https://twitter.com/LongDesertTrain/status/1600559000155979776
… when it comes to creating interesting new viral mutants

Are We Living Under ‘Technofeudalism’?
https://nymag.com/intelligencer/2022/10/what-is-technofeudalism.html
I’d guess so

Mental Illness Is Not in Your Head
https://www.bostonreview.net/articles/mental-illness-is-not-in-your-head/
It’s usually a bit more complex

70th Birthday Bhante Bodhidhamma’s Life story
https://www.youtube.com/watch?v=13_U9VMqFRA10
From Pete from Manchester to Bhante in Burma

Give Your Ideas Some Legs: The Positive Effect of Walking on Creative Thinking
https://www.apa.org/pubs/journals/releases/xlm-a0036577.pdf

Irina Rimes – Depre El
https://music.youtube.com/watch?v=OCmgKihQdeA&feature=share
I quite like that

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 Berlin Digital Science for Drug Discovery Meetings, please just let me know, cheers!

Best wishes,

Andreas

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