Dear All,
I would like to circulate some current Cheminformatics- (and related) news to everyone as follows. If you have information from your side for distribution please just let me know, and I am very happy to include it on the next occasion.
So here we go…
Events
9-18 August 2022
Biological Data Science Summer Workshop 2022
Virtual Event
https://tinyurl.com/drc-biods-workshop-2022
7 September 2022
Cambridge Cheminformatics Meeting – programme and registration available shortly, mark the date!
Cambridge Crystallographic Data Centre (CCDC) and on Zoom (Hybrid)
http://c-inf.net/
14 September 2022
Simulating Cellular Biology to Facilitate Development of Precision Oncology
Virtual Event
https://www.eventbrite.co.uk/e/simulating-cellular-biology-to-facilitate-development-of-precision-oncology-tickets-385603850497
15/16 September 2022
Machine Intelligence for Quantitative Modeling in Drug Discovery & Development Applications
Virtual Event
https://register.gotowebinar.com/register/8931548880813393420?source=IQ+LinkedIn
26-30 September 2022
23rd European Symposium on Quantitative Structure-Activity Relationship (EuroQSAR)
Heidelberg, Germany
https://www.euroqsar2022.org/
20 October 2022
Discngine Meetup 2022
Virtual Event
https://www.discngine.com/discngine-meetup-2022
23 November 2022
SCI-RSC Workshop on Computational Tools for Drug Discovery 2022
Birmingham, UK
https://www.soci.org/events/fine-chemicals-group/2022/scirsc-workshop-on-computational-tools-for-drug-discovery-2022
Jobs
Postdoctoral Fellow Computational Chemistry and Principal Scientist Data Science
Johnson&Johnson
Antwerp, Belgium / worldwide
https://www.linkedin.com/jobs/view/3158642854
https://www.linkedin.com/jobs/view/3181581525
Senior Principal Scientist CADD
UCB
Brussels, Belgium
https://www.linkedin.com/jobs/view/3139717593
Computational Chemist/Computer Scientist
AstraZeneca
Molndal, Sweden
https://www.linkedin.com/jobs/view/3156264484
Computational Chemist / Molecular Modeller / Cheminformatician
Nuvisan
Berlin, Germany
https://www.linkedin.com/jobs/view/3141006556
Principal Computational Chemist
Evotec
Abingdon, UK
https://www.linkedin.com/jobs/view/3164810534
Computational Drug Design Scientist
Acellera
Barcelona, Spain
https://www.linkedin.com/jobs/view/3178055395
Chief Technology Officer, Research Scientists, Director of Research, Software Engineers, …
Optibrium
Cambridge, UK
https://optibrium.com/careers/
Postdoctoral Researcher
Sano Centre for Computational Medicine
Cracow, Poland
https://www.linkedin.com/jobs/view/3158286504
Small-Molecule AI Scientist
Roche
Basel, Switzerland
https://www.linkedin.com/jobs/view/3171164941
Partnership Manager – Life Science Data and Models
Evolvus
Europe/East Coast/West Coast/Hybrid
http://www.drugdiscovery.net/data/evolvus_partnershipmanager.pdf
Computational Chemist for Drug Discovery
LEO Pharma
Ballerup, Denmark
https://www.linkedin.com/jobs/view/3173342200
Cheminformatics Data Scientist, Discovery Science Team Leader, Research and Applications Scientists, …
Cambridge Crystallographic Data Centre
Cambridge, UK
https://www.ccdc.cam.ac.uk/theccdcprofile/careers/
Postdoctoral Research Scientist – Bioinformatician in omics
Bayer
Sophia, France
https://jobs.bayer.com/job/Sophia-Postdoctoral-Research-Scientist-Bioinformatician-in-omics-%28mfd%29-Alpe/825821401/
Postdoctoral Researcher in Computational Chemistry
ETH
Zurich, Switzerland
https://www.jobs.ethz.ch/job/view/JOPG_ethz_AuVTV9U4V2SIWwCTZI
Cheminformatics Scientist, Bioinformatics Scientist AI/ML
MSD
Prague, Czechia
https://www.linkedin.com/jobs/view/3175177073
https://www.linkedin.com/jobs/view/3175174395
Cheminformatics…
“The AlphaFold2 structures show comparable early enrichment of known active compounds to apo structures[…]”
https://doi.org/10.26434/chemrxiv-2022-kcn0d
Science lives from…
“Most AlphaFold2 models are not compatible with binding of ligands in the set of 50 GPCR binding sites”
https://twitter.com/raintank2010/status/1541965826189774849
… discussion and controversy, as well as understanding the applicability domain of methods; and (sometimes), even advances this way …
“When Virtual Screening Yields Inactive Drugs: Dealing with False Theoretical Friends”
https://doi.org/10.1002/cmdc.202200278
… as long as we remember to validate computational prediction with experiment.
RSC CICAG Newsletter Summer 2022
http://www.rsccicag.org/index_htm_files/CICAG%20Newsletter%20Summer%202022%20FINAL.pdf
What happened, happens, and is going to happen at the RSC Chemical Information and Computer Applications Group
Synthesis-Aware Generation of Structural Analogues
https://pubs.acs.org/doi/10.1021/acs.jcim.2c00246
But can I also make all analogues the same way? The implementation (in NAOMI ChemBio Suite) is available, free for academics and evaluation purposes, at https://software.zbh.uni-hamburg.de/
WebMolKit – a “Cheminformatics toolkit built with TypeScript. Can be used to carry out some fairly sophisticated cheminformatics tasks on a contemporary web browser, such as rendering molecules for display, format conversions, calculations, interactive sketching, among other things”
https://cheminf20.org/2022/07/26/webmolkit-now-with-apache-for-all
Thanks Alex (Clark)!
… Beyond Cheminformatics …
“Why do tree-based models still outperform deep learning on tabular data?”
https://twitter.com/GaelVaroquaux/status/1549422403889106944
Observed before empirically, but here properly investigated
“An approachable, flexible and practical machine learning workshop for biologists”
https://www.biorxiv.org/content/10.1101/2022.02.03.479008v2
Also very suitable for chemists from what I can see; we need to bridge ML/AL and the life sciences better to really advance the field
“Deep Learning for Molecules & Materials”
https://dmol.pub/
A free online book and resource on the above, by Andrew D. White
“Python tutorial on Conformal Prediction”
https://twitter.com/gabrielpeyre/status/1544294291752865793?t=wWQ91gnLlegVligroC8f7w&s=19
by Gabriel Peyre
Lex Fridman Podcast with Demis Hassabis, of DeepMind
https://open.spotify.com/episode/1zcT7fUeArhjU8J7weCzvG
Including sections on AlphaFold, Quantum simulation, Physics and others
Preclinical assay checklist for oral small molecule candidates for drug development
https://www.rgdscience.com/index.php/assay-guidelines/
&
Molecular Descriptors & Ligand Efficiency Metrics Table
https://www.rgdscience.com/index.php/molecular-descriptors-ligand-efficiency-metrics/
(both courtesy of Tim Ritchie)
“Tools for science”
https://docs.google.com/document/d/1jBGk-u5auVCvI5EMaQnptMWbxHHl3ncIhKgIgEzjylw/edit
How to give a talk, write a paper and a rebuttal letter, how to review a paper… various resources
Richard Feynman’s Lectures on Physics
https://twitter.com/Rainmaker1973/status/1543920688632922115?t=rPasYWYuazt5wn73xLndjQ&s=19
His videos are also very much worth watching, e.g. on “Knowing vs Understanding” (and others)
https://www.youtube.com/watch?v=NM-zWTU7X-k&list=PLyQSN7X0ro23NUN9RYBP5xdBYoiv2_5y2&index=3
… and clearly beyond Cheminformatics
“He Dropped Out to Become a Poet. Now He’s Won a Fields Medal.”
https://www.quantamagazine.org/june-huh-high-school-dropout-wins-the-fields-medal-20220705/
“In 2013, he decided he wanted to learn to cook. As a total beginner, he adopted the strategy of making the same dish — a simple pasta in oil — every day until it was perfect. For six months, that’s exactly what he did.”
Physicists doing a cycling race
https://twitter.com/visevic/status/1544213709291229184?t=x00U8071r9p_C-9OaNiPRQ&s=19
If it works – it works.
“Druglike is building a decentralized computing network which provides resources for anyone looking to start or contribute to early-stage drug discovery projects.”
https://www.newswire.com/news/announcing-druglike-a-web3-drug-discovery-platform-21779057
The new project by Martin Shkreli, just two months out of prison
https://www.thedailybeast.com/pharma-dirtbag-martin-shkreli-now-wants-to-disrupt-the-drug-biz
“Business Retreats and Sanctions Are Crippling the Russian Economy”
https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4167193
Some facts in the often fact-free news landscape
As explored in more detail over the last month I learned that Bob Marley‘s ‘at least 11[1]-12[2] children’ basically all did music as well, e.g.
Ky-Mani Marley, ‘Rasta Love’
https://music.youtube.com/watch?v=AkWXXGe49cw
Stephen Marley, ‘Inna di Red’
https://music.youtube.com/watch?v=xQwtjkMnaNo
[1] https://en.wikipedia.org/wiki/Bob_Marley
[2] https://jamaicans.com/meet-bob-marleys-12-children/
That being said, I also spent some time with Mulatu Astatke, and the Heliocentrics, again recently, this music really detaches me from everyday life:Mulatu Astatke & The HeliocentricsEsketa Dance
https://music.youtube.com/watch?v=6qVTHGraEFY
(A friend of mine got married in Addis Ababa 10 years ago, and I still vividly remember the live music session in the local corner bar I randomly walked into that time… Ethiopia had/has a very vivid music scene which I wasn’t really aware of before.)
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