Dear All,
I would like to circulate some current Cheminformatics- (and related) news to everyone as follows.
In particular, I would like to mention the In Silico Toxicology Meeting in Cambridge on 6 November, the first EFMC2 ‘Tandem Talk’ (a modeller presenting together with a medicinal chemist) on 28 November, the Berlin Digital Sciences for Drug Discovery Meeting on 29 November, and the next Cambridge Cheminformatics Meeting on 6 December. For all of those events also an option for virtual attendance is provided, for details please see below.
So here we go…
Events
6 November 2023
In Silico Toxicology Network Meeting 2023: In Silico Toxicology – From Omics to Virtual Twins
Organized by the Cambridge Alliance for Medicines Safety
Cambridge, UK and Virtual (Hybrid)
https://www.eventbrite.co.uk/e/insilico-toxicology-symposium-cambridge-alliance-on-medicines-safetycams-tickets-728735997987
6-10 November 2023
OpenTox Virtual Conference 2023
Virtual Event
https://www.opentox.net/events/virtual-conference-2023/program
7 November 2023
Automated Intelligent Chemistry
London, UK
https://www.soci.org/events/young-chemists-panel/2023/automated-intelligent-chemistry
20-22 November 2023
EU-OpenScreen Autumn Training School
Topics: Assay development, hit selection, quality control, hit to lead, …
Virtual Event
https://www.eu-openscreen.eu/services/training/autumn-training-school-2023.html
24 November 2023
27th MGMS Young Modellers’ Forum 2023
Oxford, UK
https://www.mgms.org/WordPress/conferences/ymf-2023
28 November 2023
EFMC2 Tandem Talks
Real World Use of FEP+ Calculations – Lessons Learned at Boehringer Ingelheim
Virtual Event
https://www.efmctandemtalks.org
29 November 2023
Berlin Digital Science for Drug Discovery Seminars
Berlin, Germany and on Zoom (Hybrid)
More information: http://www.digidrug.net
Direct Zoom registration: https://cam-ac-uk.zoom.us/meeting/register/tZUvdOmqrzguHdTF4JvycBLCpYNyT_DLY8-5
Programme
Machine Learning for Drug Discovery With Low-Data: Challenges and Opportunities
Francesca Grisoni, TU Eindhoven
https://research.tue.nl/en/persons/francesca-grisoni
Second Speaker TBC – please just let me know if you are interested to present on this or a future occasion!
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
8 December 2023
ELLIS Machine Learning for Molecule Discovery Workshop
Virtual Event
https://www.eventbrite.com/e/ellis-machine-learning-for-molecule-discovery-workshop-tickets-723480107477
11-15 December 2023
2nd BioHackathon Germany
Bielefeld, Germany
https://www.denbi.de/de-nbi-events/1547-biohackathon-germany-2jobs
7 March 2024
Conformational Design in Drug Discovery 2024
Stevenage, UK
https://macinchem.org/2023/10/16/conformational-design-in-drug-discovery-2024
22-26 September 2024
24th EuroQSAR
Barcelona, Spain
https://www.euroqsar.org
Jobs
Director, Cheminformatics – In Silico Discovery
Johnson & Johnson
Beerse, Belgium
https://www.linkedin.com/jobs/view/3713608892
Computational Chemistry and ML/AI
Bayer
Lyon, France
https://www.linkedin.com/jobs/view/3741760457
Cheminformatician
NovaMechanics Ltd
Nicosia, Cyprus
https://www.linkedin.com/jobs/view/3741421025
Lecturer/Reader in Biomedical Artificial Intelligence
University of Edinburgh
Edinburgh, UK
https://elxw.fa.em3.oraclecloud.com/hcmUI/CandidateExperience/en/sites/CX_1001/job/8819
Senior Data Scientist | Cheminformatics and Computational Chemistry
molab.ai
Munich, Germany or remote
https://www.linkedin.com/jobs/view/3744780346
Director of Cheminformatics & Computational Chemistry, Principal Computational Chemist
BenevolentAI
London, UK
https://www.linkedin.com/jobs/view/3741649833
https://www.linkedin.com/jobs/view/3741652386
Associate Director, Computational Chemistry
Insmed Inc.
Cambridge, UK
https://www.linkedin.com/jobs/view/3709493622
Head of Biomedical Data Science
Bayer
Wuppertal, Germany
https://www.linkedin.com/jobs/view/3658348802
Computational Chemist
SoseiHeptares
Cambridge, UK
https://cezanneondemand.intervieweb.it/heptares/jobs/computational-chemist-35980/en
Computational Medicinal Chemist/Senior Expert Data Science
Novartis
Cambridge, MA
https://www.novartis.com/careers/career-search/job-details/385500br/computational-medicinal-chemistsenior-expert-data-science
Scientific Software Developers for Drug Discovery; Computational Drug Discovery Opportunities
D. E. Shaw Research
New York, NY
https://www.linkedin.com/jobs/view/3733381037
https://www.linkedin.com/jobs/view/3733373666
Tenure Track Assistant or Associate Professor Computer-Aided Drug Design
Groningen University
Groningen, Netherlands
https://www.linkedin.com/jobs/view/3727233660
Head of External Innovation Computational Biology and Digital Sciences.
Boehringer Ingelheim
Biberach, Germany
https://www.linkedin.com/jobs/view/3750421204
Postdoc, Structure-Based Drug Design
Uppsala University
Uppsala, Sweden
https://www.jobb.uu.se/details/?positionId=671379
Ph. D. Position in Cheminformatics: Big Data and Artificial Intelligence
University of Bern
Bern, Switzerland
https://gdb.unibe.ch/positions
Data Scientist Intern
Aqemia
Paris, France
https://www.linkedin.com/jobs/view/3712725790
Machine Learning Scientist, Founder’s Associate, Working Student
Cinference
Berlin, Germany
https://cinference.notion.site/CINFERENCE-JOB-BOARD-9d4bbf6930894576ad8ef32e867ae4a7
Cheminformatics…
New version of ProLIF
https://github.com/chemosim-lab/ProLIF/releases/tag/v2.0.0
From MD trajectories to interaction fingerprints (https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00548-6)
Lig3DLens: An open source ligand-based 3D virtual screening toolbox
https://healx.ai/lig3dlens-an-open-source-ligand-based-3d-virtual-screening-toolbox
Based on conformational alignment and electrostatic similarity
Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom
https://www.biorxiv.org/content/10.1101/2023.10.09.561603v1
“a deep network capable of modeling full biological assemblies containing proteins, nucleic acids, small molecules, metals, and covalent modifications given the sequences of the polymers and the atomic bonded geometry of the small molecules and covalent modifications”
Related work from Isomorphic Labs:
https://www.isomorphiclabs.com/articles/a-glimpse-of-the-next-generation-of-alphafold
ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation
https://arxiv.org/abs/2309.05853
First generating molecules was in 2D, then 3D, and now it is becoming targeted towards particular binding partners
New consulting/service company of a former colleague of mine: SciPharma Informatics
www.scipharmainformatics.com
…is dedicated to facilitating the digital transformation of laboratories within the Pharma, Biotech, Life Science, and Healthcare sectors. Our unique strength lies in a deep understanding of the business processes specific to these industries and a mastery of Informatics solutions for digitalizing and automating processes and data generated within laboratories. Services include Requirement analysis, Business analysis, Evaluation of software solutions, RFP/RFI process, Implementation, Interfacing multiple laboratory software systems, Consulting in Data governance and FAIR Data management, Project management, supporting Validation and UATs
… beyond cheminformatics …
Illumina: The Measurement Monopoly
https://centuryofbio.com/p/illumina
There is the science… and there is the business you build on top of it
Mapping global dynamics of benchmark creation and saturation in artificial intelligence
https://arxiv.org/abs/2203.04592
Did we reach the pinnacle already then?
Best Practices for QSAR Model Reporting: Physical and Chemical Properties, Ecotoxicity, Environmental Fate, Human Health, and Toxicokinetics Endpoints
https://pubmed.ncbi.nlm.nih.gov/30561225
A reminder to do things properly… ‘Altogether, 42.5% of the reviewed articles were found to be potentially reproducible’…which is potentially not even half of all articles
Assessing public forecasts to encourage accountability: The case of MIT’s Technology Review
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183038
Predicting the future turns out to be non-trivial
“Low-Resource” Text Classification: A Parameter-Free Classification Method with Compressors
https://aclanthology.org/2023.findings-acl.426
Deep Neural Networks vs GZIP
AI hype is built on high test scores. Those tests are flawed.
https://www.technologyreview.com/2023/08/30/1078670/large-language-models-arent-people-lets-stop-testing-them-like-they-were
Testing humans and algorithms needs different approaches
Nextflow Summit 2023 Barcelona, Recordings available
https://www.youtube.com/playlist?list=PLPZ8WHdZGxmUotnP-tWRVNtuNWpN7xbpL
Workflows using containers – for programme see https://summit.nextflow.io/barcelona/agenda/summit/#events
… and clearly beyond cheminformatics
The NID Tapes: Electronic Music From India 1969-1972
https://pitchfork.com/reviews/albums/various-artists-the-nid-tapes-electronic-music-from-india-1969-1972
https://www.youtube.com/watch?v=_-Nyr2rFhEE&list=PL1jMKWiJjnPdI-FOirhR995hjNMzbnNff
Didn’t come across this before – you can really hear the playful discovery of something new in the songs
Today’s choice of Herman ze German … duese im Sauseschritt
https://music.youtube.com/watch?v=HaPAqh37NTk
Yes, that’s what music videos looked like in 1983 (at least in Germany…)
Global warming in the pipeline
https://academic.oup.com/oocc/article/3/1/kgad008/7335889
More isn’t always better (and here quite clearly it isn’t)
How we became obsessed with wellness
https://www.theguardian.com/wellness/2023/nov/01/wellness-industry-healthcare-women-stress
Wellness, influencers, the metaverse… times have changed since I was a boy!
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