Sign in

Gerard JP van Westen

@gjpvwesten.bsky.social
1.6K followers 69 following 57 posts

KNCV Gold Medal 2023. Exploring drug space with AI 💪, Professor of AI & Med Chem in Leiden, Computational Drug Discovery, cddl.nl, Opinions are my own.

PostsRepliesMedia
Reposted by Gerard JP van Westen
Chris Aalberts @chrisaalberts.bsky.social · 27/07/2026
Goed onderzoek over de noodzaak van alternatieve media, waar inmiddels overigens ook wel eisen aan gesteld mogen worden. chrisaalberts.nl/2026/07/24/a...
chrisaalberts.nl
Alternatieve media zijn broodnodig, tijd om ze serieus te nemen  - Chris Aalberts
Alternatieve media zijn overal, maar zinnig onderzoek ernaar is schaars. Onlangs las ik een wetenschappelijk artikel waarin werd beweerd dat het erg ingewikkeld is geworden om te bepalen wat journalis...
011
Reposted by Gerard JP van Westen
Bert Hubert NL 🇺🇦🇪🇺🇺🇦 @bert-hubert.mastodon.nl.ap.brid.gy · 10/09/2025
@ionica (en de discussie op www.toughpigs.com/i-can-assure-you-… is ook goed!)
Her: Name your favorite literary vampire.
Me: The one from Sesame Street.

Her: He doesn't count.

Me: | can assure you that he does.
0133
Reposted by Gerard JP van Westen
Noel Research Group @noelgroupuva.bsky.social · 10/07/2025
New @chemrxiv.bsky.social preprint! RoboChem-Flex is a powerful, low-cost (<5k EUR), modular self-driving lab for chemical synthesis We showcase 6 studies (photochemistry, biocatalysis, cross coupling, ee ...), all optimized with different configurations & ML 🔗 chemrxiv.org/engage/chemr...
37321
Reposted by Gerard JP van Westen
ICCS @intconfchemstr.social.edu.nl.ap.brid.gy · 23/05/2025
we are very happy to relay that the CSA Trust has decided to award the Mike Lynch award to Prof. Val Gillet who will be giving a keynote lecture at our #ICCS2025 opening session csa-trust.org/2025/05/23/mike-lynch…
csa-trust.org
Mike Lynch Award 2025: Val Gillet
In recognition of her pioneering research in chemical structure analysis, visionary educational leadership, and enduring dedication to advancing scientific collaboration, Professor Val Gillet has been awarded the 2025 Mike Lynch Award by the Trustees of the CSA Trust. The Trustees are proud to honor Professor Gillet for her outstanding and innovative contributions to the field of Chemoinformatics. Her influential body of work – widely cited and highly regarded – has shaped the Chemoinformatics landscape and driven progress in pharmaceutical research and development. In parallel with her research achievements, Professor Gillet has played a central role in building and refining the Chemoinformatics educational program at the University of Sheffield. Under her supervision, the program has earned international recognition as a hub of excellence for research and training. She is also co-author of a foundational textbook that remains a key reference in the field. Beyond her academic accomplishments, Professor Gillet has been instrumental in fostering collaboration and visibility within Chemoinformatics. Her longstanding support of the Cheminformatics Conference in Sheffield and the International Conference on Chemical Structures in Noordwijkerhout has helped elevate them to the field’s most prominent international gatherings. Val Gillet is a Professor of Chemoinformatics at the University of Sheffield, where she leads the Chemoinformatics Research Group within School of Information, Journalism and Communication. https://www.linkedin.com/in/val-gillet-15a60429/ https://www.sheffield.ac.uk/ijc/people/val-gillet The CSA Trust is an internationally recognized, registered charity that promotes education, research, and development in fields related to chemical structures and cheminformatics. ### Share this: * Click to share on X (Opens in new window) X * Click to share on Facebook (Opens in new window) Facebook * Like Loading... ### _Related_
021
Reposted by Gerard JP van Westen
ICCS @intconfchemstr.social.edu.nl.ap.brid.gy · 05/06/2025
the next International Conference on Chemical Structures, edition 14, will be held in the week of June 11-15 2028! #ICCS2025 #ICCS2028
Photo of Gerard van Westen on stage and the "Save the Date!" slide announcing ICCS 2028, from June 11th to June 15th and the hashtag for that meeting: #ICCS2028
013
Reposted by Gerard JP van Westen
Stephan Hacker @stephanhacker2.bsky.social · 14/03/2025
Come and join us for an other exciting @led3hub.bsky.social Lecture by @jpoverington.bsky.social on March 27th.
051
Gerard JP van Westen @gjpvwesten.bsky.social · 12/03/2025
Looking forward to these talks!
031
Gerard JP van Westen @gjpvwesten.bsky.social · 12/03/2025
#NietDeSpeld… toch @speld.nl ? “Bedrijven in de duurzame energiesector willen uitzondering stikstofregels” nos.nl/artikel/2559...
nos.nl
Bedrijven in de duurzame energiesector willen uitzondering stikstofregels
Het kabinet zou bij de bouw van duurzame energieprojecten een uitzondering moeten maken op de stikstofregels, vinden betrokken bedrijven.
000
Gerard JP van Westen @gjpvwesten.bsky.social · 11/03/2025
The latest from CDD Leiden! Towards assay-aware bioactivity model(er)s: getting a grip on biological context We show how including assay descriptors in PCM models improves performance. chemrxiv.org/engage/chemr...
031
Gerard JP van Westen @gjpvwesten.bsky.social · 05/03/2025
It is time…
010
Reposted by Gerard JP van Westen
ICCS @intconfchemstr.social.edu.nl.ap.brid.gy · 01/03/2025
We are very happy to inform you all that we received > 160 abstracts for the upcoming ICCS! From the submissions the program committee and the scientific advisory board will select around 30 papers for the plenary sessions. All submissions that cannot be included in the plenary sessions will be […]
social.edu.nl
Original post on social.edu.nl
043
Gerard JP van Westen @gjpvwesten.bsky.social · 27/02/2025
The ICCS has currently close to 100 submitted abstracts and already over a 100 registrations. There is 1 day left to submit an abstract after which the SAB will review them for an exciting program. #ICCS2025 See you there? iccs-nl.org
iccs-nl.org
ICCS – International Conference on Chemical Structures
000
Gerard JP van Westen @gjpvwesten.bsky.social · 22/02/2025
Goed stuk geschreven door collega Sense Jan vd Molen. www.mareonline.nl/opinie/angst...
mareonline.nl
Angstcultuur aan de academie is onacceptabel
Protest hoort bij het Praesidium Libertatis. Maar als Joodse studenten niet meer naar college durven, botst dat met alle academische idealen en vrijheden, betoogt Sense Jan van der Molen.
000
Gerard JP van Westen @gjpvwesten.bsky.social · 17/02/2025
NIH peer review percentile scores are poorly predictive of grant productivity. "...observations suggest that despite the ability of reviewers to discriminate between strong grant applications and the remainder, they have limited ability to predict future productivity..." doi.org/10.7554/eLif...
030
Gerard JP van Westen @gjpvwesten.bsky.social · 15/02/2025
The ICCS website is updated with the preliminary program. Have a look! Registration (via conftool) is also opened. Remember the abstract deadline is Feb 28th ..! iccs-nl.org/general-info...
030
Gerard JP van Westen @gjpvwesten.bsky.social · 15/02/2025
We're starting to have a conference! Very much looking forward to this event... CC: @led3hub.bsky.social
030
Gerard JP van Westen @gjpvwesten.bsky.social · 06/02/2025
Now viewing the talk of Kelly Chibale part of the #LED3LUCID symposium in honor of the @unileiden.bsky.social 450 year dies natalis.
011
Reposted by Gerard JP van Westen
Stephan Hacker @stephanhacker2.bsky.social · 06/02/2025
Insightful talk by Miquel Duran-Frigola at the #LED3LUCID Symposium. He talked about making powerful computational tools available to researchers in the Global South through the Ersilia Open Source Initiative. (1/3) www.nature.com/articles/s41...
242
Reposted by Gerard JP van Westen
Stephan Hacker @stephanhacker2.bsky.social · 06/02/2025
How do the structure and the dynamics of proteins dictate their molecular function? In her @led3hub.bsky.social Keynote Lecture at the #LED3LUCID Symposium, Paola Picotti gave insights into her group's amazing research in this field. Great insights into the use of LiP-MS-based proteomics. (1/6)
183
Reposted by Gerard JP van Westen
Stephan Hacker @stephanhacker2.bsky.social · 06/02/2025
How can we efficiently explore the vast chemical space for drug discovery? In his talk at the #LED3LUCID Symposium, @gjpvwesten.bsky.social of the @led3hub.bsky.social talked about how his group uses the power of AI to contribute to the solution of this challenge. (1/4)
173
Gerard JP van Westen @gjpvwesten.bsky.social · 01/02/2025
Dit is toch de kip met de gouden eieren slachten? Deze promovendi vormen bij mijn weten geen netto kosten post maar een baten post over de hele looptijd… www.mareonline.nl/nieuws/uni-w...
mareonline.nl
Universiteit wil vaste tarieven voor beurs- en buitenpromovendi
Het college van bestuur wil dat beurs- en buitenpromovendi een vast bedrag gaan betalen. Ook worden PhD’s die te weinig geld meebrengen geweerd. ‘Wordt dit gebruikt om de gehate bezuinigingen op te va...
001
Gerard JP van Westen @gjpvwesten.bsky.social · 30/01/2025
Can someone tell me why I can only update @microsoft.com office software on my mac if I allow autoupdate to launch at startup? why not enabling is called a problem? why I can only get rid of this prompt by killing autoupdate in system monitor? Very bad behavior but typical ...
110
Gerard JP van Westen @gjpvwesten.bsky.social · 30/01/2025
We have set-up and tested an integrated coding environment for students at LACDR. Using the noteable platform, integrated with Brightspace, teach them coding in R and Python via Jupyter notebooks (including docking and 3D!) Reach out we want to share! www.staff.universiteitleiden.nl/news/2025/01...
staff.universiteitleiden.nl
LACDR introduces ‘Digital Labcoat’ for Biopharmaceutical Sciences students - Leiden University
Learn to program, gain knowledge of AI methods, or use it in a research project at the LACDR. With the introduction of the innovative digital learning environment ‘Digital Labcoat’, Biopharmaceutical ...
042
Gerard JP van Westen @gjpvwesten.bsky.social · 29/01/2025
Looking forard to this event next week! LSBP The Future of Health Congress leidenbiosciencepark.nl/events/the-f...
leidenbiosciencepark.nl
The Future of Health Congress
020
Gerard JP van Westen @gjpvwesten.bsky.social · 28/01/2025
The ICCS website is updated with the preliminary program. Have a look! Registration (via conftool) is also already opened. Remember the abstract deadline is valentine's day (Feb 14th) ..! iccs-nl.org/general-info...
040
Reposted by Gerard JP van Westen
Rachel Thomas @math-rachel.bsky.social · 24/01/2025
Some mistakenly believe AI can easily create magic solutions, without understanding the need for high-quality data. The success of AlphaFold was made possible by 50 years of prior work gathering protein structures into a rich database (Protein Data Bank launched in 1971) 3/
NATURE NEW BIOLOGY VOL. 233 OCTOBER 20 1971
CRYSTALLOGRAPHY
Protein Data Bank
A repository system for protein
crystallographic data will be oper-
ated jointly by the Crystallographic
Data Centre, Cambridge, and the
Brookhaven National Laboratory.
The system will be responsible for
storing atomic coordinates, structure
factors and electron density maps
and will make these data available
on request. Distribution will be
on magnetic tape in machine-read-
able form whenever possible. There
will be no charge for the service
other than handling costs. Files
2258
Gerard JP van Westen @gjpvwesten.bsky.social · 25/01/2025
One of the most hilarious developments. Windows 11 requires new PCs (TPM & CPU requirements technically not needed), hence responsible for the largest eWaste collection. Yet, tells me to make my carbon footprint lower using power features... #greenwashing www.canalys.com/insights/end...
030
Gerard JP van Westen @gjpvwesten.bsky.social · 22/01/2025
I am looking for a good PDF editor (can be paid). Been using Adobe for years but the overhead, the delay launching the software to check the digital license, the terms of service controversy (lnkd.in/ehJsjDu6). (!) all these processes simply to be able to edit a pdf...(!)
120
Reposted by Gerard JP van Westen
Leiden Early Drug Discovery & Development (LED3) @led3hub.bsky.social · 17/01/2025
We are happy that @mvdstelt.bsky.social represented our network with a keynote lecture at the Netherlands Proteomics Platform winter meeting #NPP2025. He presented his group's important work on better understanding the function of the human brain on a molecular level in health and disease.
072
Gerard JP van Westen @gjpvwesten.bsky.social · 17/01/2025
If you are interested in #AI and #DrugDiscovery, attend the upcoming ICCS June 1st - Jun 5th in Noordwijkerhout! Last call for papers. Please repost! Registration and abstracts (deadline 14 Feb): iccs-nl.org/general-info...
396
Reposted by Gerard JP van Westen
Leiden Early Drug Discovery & Development (LED3) @led3hub.bsky.social · 16/01/2025
We are happy that Kelly Chibale will give a lecture within our Faculty-wide Tuesday Talk Series on February 4th at 4 p.m. in room CM1.26: "Tailoring medicines for the genetically diverse African populations". Free registration required. www.medewerkers.universiteitleiden.nl/agenda/2025/...
021
Gerard JP van Westen @gjpvwesten.bsky.social · 16/01/2025
Very interesting work. Not only sequence to 3D, but also function to sequence and more… Simulating 500 million years of evolution with a language model www.science.org/doi/10.1126/...
science.org
Simulating 500 million years of evolution with a language model
More than three billion years of evolution have produced an image of biology encoded into the space of natural proteins. Here we show that language models trained at scale on evolutionary data can gen...
141
Gerard JP van Westen @gjpvwesten.bsky.social · 03/01/2025
Hear hear! www.science.org/content/arti...
020
Gerard JP van Westen @gjpvwesten.bsky.social · 24/12/2024
I am looking for a technician in Artificial Intelligence and computational drug discovery. You will be in my team with Oncode Accelerator (AI Platform). Come join us, we have cake and GPUs! Details: www.universiteitleiden.nl/vacatures/20... CC: @led3hub.bsky.social , @unileiden.bsky.social
universiteitleiden.nl
Technician in Artificial Intelligence and computational drug discovery (0.8-1.0 fte)
The Faculty of Science and the Leiden Academic Center for Drug Research are looking for a Technician in Artificial Intelligence and computational drug discovery (0.8-1.0 fte) Project description Withi...
31412
Reposted by Gerard JP van Westen
Science News @scinews.bsky.social · 22/12/2024
MIT researchers introduce Boltz-1, a fully open-source model for predicting biomolecular structures With models like AlphaFold3 limited to academic research, the team built an equivalent alternative, to encourage innovation more broadly www.eurekalert.org/news-release...
eurekalert.org
MIT researchers introduce Boltz-1, a fully open-source model for predicting biomolecular structures
Researchers in the MIT Jameel Clinic for Machine Learning in Health developed a fully open-source biomolecular structure prediction model that achieves state-of-the-art performance, at the level of Al...
08428
Gerard JP van Westen @gjpvwesten.bsky.social · 22/12/2024
Ik kan hier echt met mn kop niet bij… nos.nl/artikel/2548...
nos.nl
60 dierenactivisten in hoger beroep vrijgesproken voor bezetten varkensstal Boxtel
Het gerechtshof concludeert dat niet bewezen kan worden dat de dierenactivisten de staldeuren hebben geforceerd om binnen te komen.
000
Gerard JP van Westen @gjpvwesten.bsky.social · 21/12/2024
Very interesting work! Simulate at 600-1000 K and see how long each ligand can hold on. Fast (100 fold faster than FEP) and no requirement for congeneric series as with FEP, while performing similar. Still only really tested on kinases…Would be fun to give this a spin… pubs.acs.org/doi/full/10....
pubs.acs.org
ModBind, a Rapid Simulation-Based Predictor of Ligand Binding and Off-Rates
In rational drug discovery, both free energy of binding and the binding half-life (koff) are important factors in determining the efficacy of drugs. Numerous computational methods have been developed ...
092
Reposted by Gerard JP van Westen
Remco Breuker 🟥 @remcobreuker.bsky.social · 11/12/2024
Geslaagde #WOinActie demonstratie met fluitconcert bij Lipsius in Leiden. Er was nog een demonstratie in Leiden bij het Pieter de la Court.
07413
Reposted by Gerard JP van Westen
Stephan Hacker @stephanhacker2.bsky.social · 10/12/2024
Great EScience event of our Factulty of Science. Researchers that develop AI methods, including @gjpvwesten.bsky.social of the @led3hub.bsky.social, presented their research and discussed, how AI can be used in diverse other research areas in the faculty. www.universiteitleiden.nl/en/events/20...
032
Reposted by Gerard JP van Westen
Volker Weber @vowe.net · 07/12/2024
What a time to be alive
413065378
Gerard JP van Westen @gjpvwesten.bsky.social · 03/12/2024
Check out QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool. Fully compatible with PCMol and DrugEx and available for download freely (python). #qsar #ai #cheminformatics Paper: jcheminf.biomedcentral.com/articles/10.... Code: github.com/CDDLeiden/QS...
jcheminf.biomedcentral.com
QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool - Journal of Cheminformatics
Building reliable and robust quantitative structure–property relationship (QSPR) models is a challenging task. First, the experimental data needs to be obtained, analyzed and curated. Second, the numb...
080
Gerard JP van Westen @gjpvwesten.bsky.social · 30/11/2024
Tweakers leden dag..!
020
Reposted by Gerard JP van Westen
Peter Kenny @pwk2024.bsky.social · 28/11/2024
Fearon et al (2024) Accelerating #DrugDiscovery With High-Throughput #Crystallographic #Fragment Screening and Structural Enablement. Appl Res e202400192 #FBLD #FBDD #DrugDesign #MedChem #StructBiol #OpenAccess #chemsky 🧪 doi.org/10.1002/appl...
doi.org
Accelerating Drug Discovery With High‐Throughput Crystallographic Fragment Screening and Structural Enablement
Crystallographic fragment screening has become highly efficient, overcoming previous challenges of low throughput and time consumption, due to advances in synchrotron technology and the establishment...
0175
Gerard JP van Westen @gjpvwesten.bsky.social · 30/11/2024
One of the most fun recent projects is our paper "AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models" by Andrius Bernatavicius. We show that the combined network learns target related chemical space. pubs.acs.org/doi/10.1021/...
pubs.acs.org
AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models
Recent advancements in deep learning and generative models have significantly expanded the applications of virtual screening for drug-like compounds. Here, we introduce a multitarget transformer model, PCMol, that leverages the latent protein embeddings derived from AlphaFold2 as a means of conditioning a de novo generative model on different targets. Incorporating rich protein representations allows the model to capture their structural relationships, enabling the chemical space interpolation of active compounds and target-side generalization to new proteins based on embedding similarities. In this work, we benchmark against other existing target-conditioned transformer models to illustrate the validity of using AlphaFold protein representations over raw amino acid sequences. We show that low-dimensional projections of these protein embeddings cluster appropriately based on target families and that model performance declines when these representations are intentionally corrupted. We also show that the PCMol model generates diverse, potentially active molecules for a wide array of proteins, including those with sparse ligand bioactivity data. The generated compounds display higher similarity known active ligands of held-out targets and have comparable molecular docking scores while maintaining novelty. Additionally, we demonstrate the important role of data augmentation in bolstering the performance of generative models in low-data regimes. Software package and AlphaFold protein embeddings are freely available at https://github.com/CDDLeiden/PCMol.
2223
Gerard JP van Westen @gjpvwesten.bsky.social · 25/11/2024
Great visualization tool. With a bit of fiddling a nice figure can be made. :) shiny.rcg.sfu.ca/u/rdmorin/sc...
010
Reposted by Gerard JP van Westen
Stephan Hacker @stephanhacker2.bsky.social · 25/11/2024
Sadly, there will be no @led3hub.bsky.social Lecture this week. Please, join us for the next one on February 6th by Paola Picotti.
073
Gerard JP van Westen @gjpvwesten.bsky.social · 25/11/2024
In the Hague protesting against the budget cuts! #woinactie
050
Gerard JP van Westen @gjpvwesten.bsky.social · 23/11/2024
Tuesday I had the honor and privilege to present my work at the royal palace to present with Max Welling and Annelien Bredenoord before the King and Queen, chaired by Marcel Levi of NWO. Once in a lifetime experience! Thankful for the invitation and the event. www.linkedin.com/feed/update/...
050