Cambridge Cheminformatics Newsletter, 7 August 2020

Dear All,

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

Events (all times where given are UK time)

12 August 2020, 2pm
Quantum Computing: A Guide for the Perplexed (online and free)
Andy Clark, IBM
http://www.ai3sd.org/summer-seminar-series-2020

19 August 2020, 2pm
Artificial Intelligence’s new clothes? From General Purpose Technology to Large Technical System (online and free)
Simone Vannuccini, University of Sussex, and Ekaterina Prytkova, Jena University
http://www.ai3sd.org/summer-seminar-series-2020

2 September 2020, 4pm
Cambridge Cheminformatics Meeting (online and free, http://www.c-inf.net for future dates)

Programme:

Towards Using Deep Generative Models for Structure-Based Design
Morgan Thomas, Centre for Molecular Informatics, University of Cambridge, and Sosei Heptares

Expanding Connectivity Between Documents, Structures and Bioactivity
Chris Southan, TW2Informatics

Registration at
https://zoom.us/meeting/register/tJEuduypqzkqHtCaYUsDkpAef1JUuzXdaQjt

28/29 September 2020
3rd AI in Chemistry (online and free)
https://www.maggichurchouseevents.co.uk/bmcs/

29/30 September 2020
Chemical Science Symposium 2020: How can machine learning and autonomy accelerate chemistry? (online and nominal fee)
https://www.rsc.org/events/detail/42791/chemical-science-symposium-2020-how-can-machine-learning-and-autonomy-accelerate-chemistry

30 September 2020
In Silico Toxicology Network Meeting (online and free)
Full programme and computational toxicology job board now online
Ca 30 places left, register soon if you wish to attend!
http://www.drugdiscovery.net/0ebp

6-16 October 2020
Drug Discovery Digital (online and free)
https://elrig.org/portfolio/drug-discovery-digital/

15 October 2020
UK QSAR Autumn 2020 Meeting (online and free)
https://go.md.catapult.org.uk/ukqsar-spring-virtual-meeting/

20-22 October 2020
American Society for Cellular and Computational Toxicology Annual Meeting (online and free)
https://www.ascctox.org/annualmeeting

Jobs

UK

Cheminformatics Software Developer and
Postdoc Artificial Intelligence and Fragment-Based Drug Discovery
Astex, Cambridge
https://astx.com/wp-content/uploads/2020/07/cheminformatics-software-developer-2020-junior-role.docx.pdf
https://www.linkedin.com/jobs/view/1981561535

Research Associate in Computational Chemistry
Newcastle University, Newcastle
https://jobs.ncl.ac.uk/job/Newcastle-Research-Associate-in-Computational-Chemistry/609354901/

Safety Data Scientist
EMBL, Hinxton
https://www.jobs.ac.uk/job/CAU675/safety-data-scientist

Head of Science
Lhasa Ltd., Leeds
https://www.lhasalimited.org/vacancies/head-of-science/6644

Postdoc Fellow – Target class artificial intelligence models
AstraZeneca, Cambridge
https://www.linkedin.com/jobs/view/1958727654/

Computational Biologist
Evotec, Abingdon
https://evotecgroup.wd3.myworkdayjobs.com/en-US/Evotec_Career_Site/job/Abingdon-Evotec/Chemical-Biologist_REQ-02093

Europe

Senior Scientist in Molecular Modelling
Novo Nordisk
Malov, Denmark
https://www.linkedin.com/jobs/view/1948229097/

Group Leader Position in Computational Pathology
Heidelberg University
Heidelberg, Germany
https://jobrxiv.org/job/heidelberg-university-hospital-27778-group-leader-position-in-computational-pathology-at-heidelberg-university/

Research Scientist – Image Analysis and AI
Evotec
Hamburg, Germany
https://evotecgroup.wd3.myworkdayjobs.com/en-US/Evotec_Career_Site/job/Hamburg/Research-Scientist–f-m-d—-Image-Analysis—AI_REQ-02073

Senior Scientist Cheminformatics
Bayer
Berlin, Germany
https://karriere.bayer.de/en/job/senior-scientist-cheminformatics-m-f-d–SF226685

PhD Candidate – AI for Drug Discovery and
Postdoctoral Researcher in Computational Drug Discovery

Leiden University
Leiden, The Netherlands
https://www.universiteitleiden.nl/vacatures/2020/q3/20-350-phd-candidate
https://www.universiteitleiden.nl/vacatures/2020/q3/20-352-postdoctoral-researcher-in-computational-drug-discovery

Research Scientist and
Full-stack developer

Pharmacelera
Barcelona, Spain
https://new.pharmacelera.com/careers/

Assorted Cheminformatics Items

Guide to Molecular Standardization (!)
https://depth-first.com/articles/2020/07/27/a-guide-to-molecular-standardization/

CICAG Newsletter for Summer 2020
https://www.rsc.org/images/CICAG_Newsletter_Summer_2020_tcm18-252147.pdf

OpenChem: A deep learning toolkit for computational chemistry and drug design
https://chemrxiv.org/articles/OpenChem_A_Deep_Learning_Toolkit_for_Computational_Chemistry_and_Drug_Design/12691943/1

Assessing the frontier: Active learning, model accuracy, and multi-objective candidate discovery and optimization
https://aip.scitation.org/doi/10.1063/5.0006124
(How to evaluate a model in the absence of large, prospective, and sufficiently diverse data sets that cover future chemical space we attempt to predict? Are we only lying into our own pocket with the current ways of ‘validating’ by showing that ‘my number is higher than yours?’ This article is worth a read for new perspectives in my opinion)

Chemical Space Exploration: How Genetic Algorithms Find the Needle in the Haystack. Interview with the Author
http://www.drugdiscovery.net/jf1u

Open invitation to contribute to a special issue ‘Artificial Intelligence in Drug Design’, for Expert Opinion in Drug Discovery
http://www.drugdiscovery.net/cnb6

… and beyond Cheminformatics

Integrating the Impact of Lipophilicity on Potency and Pharmacokinetic Parameters Enables the Use of Diverse Chemical Space during Small Molecule Drug Optimization
https://pubs.acs.org/doi/full/10.1021/acs.jmedchem.9b01813
(Bioactivity is one aspect of compound action and obviously focus of much current computational research… but how to consider PK properly? This paper shows alternative routes of how to use lipophilicity, and move away from in vitro to in vivo extrapolation, for anticipating human PK)

Machine Learning for Healthcare
Talks by Mihaela van derSchaar, at MLSS 2020, Tübingen
https://www.youtube.com/watch?v=7gvBKP61Jus&feature=youtu.be
https://www.youtube.com/watch?v=OVYNkI0PHnw&feature=youtu.be

You need to visualize (long) gene lists? Not a trivial task sometimes – Revigo might help:
http://revigo.irb.hr/

And one for the weekend: You might be aware that recently a new language model, GPT-3, was published – this is my favourite ‘validation’ I have come across so far (it literally took me half an hour longer to fall asleep that night since I couldn’t stop laughing…)
https://twitter.com/nottombrown/status/1284642771895107584

This I believe would be all from me on this occasion – have a good weekend, and if you have relevant information for me to circulate please just let me know, cheers!

Best wishes,
Andreas

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