Computational Drug Discovery Leiden

The latest bij @CDDLeiden , work from Sean M. McKenna. What if hit validation could move at the speed of your in silico ideas? We’re excited to share COMBINAUT — an automated, parallel synthesis platform designed to close the gap between virtual screening (VS) and experimental validation. chemrxiv.org/doi/full/10.26… 🔬 Built on a faculty-wide collection of in-house building blocks ⚙️ Enumerates 22.9+ million diverse synthetically accessible compounds ⏱️ Designed for parallelized synthesis in 1–32 hours 🔁 Uses repurposed solid-phase peptide synthesis equipment 🚀 Automation driven iterative hit-to-lead optimization To demonstrate the power of the platform, we targeted the allosteric pocket of C-C chemokine receptor 2 (CCR2), a key immuno-oncology target, tested ~100 hit candidates, validated diverse binders and used automation to optimize their potency. Fantastic collaboration with Sebastian Pomplun and Laura Heitman. @LACDR , @LeidenScienceEN

One of the more useful things to do with an LLM. I uploaded the conference program pdf to @NotebookLM and asked it to convert it to a .ics calendar file. Voila entire program available for import in my Symposia calendar, with names and affiliations…

RT @GJPvWesten: Impressed with Nano Banana ..!

So I printed the receptor (adenosine A2A) and the ligand (caffeine) as mesh via @MolSoft ICM. And now I can literally place the ligand in the pocket…! Printed on a @BambuLabSupport printer..

The latest by CDD Leiden: Combining Bayesian and Evidential Uncertainty Quantification for Improved Bioactivity Modeling by @BolaK_DDD pubs.acs.org/doi/10.1021/ac…

Lilly to open large production sit at the @Leidenbsp ! bnr.nl/nieuws/economi…

OPEN DEBAT IN DE WETENSCHAP! (nu met poster!) Leiden, 14 nov. met @mboudry Esmé Bosma @HofhuisSteije Elif Erken @raymondpoot @GeertenWaling. “Academische vrijheid lijkt steeds vaker onder druk te staan, door externe druk van politiek en maatschappij én door interne spanningen…”

The latest by CDD Leiden! PyVADesign: a python-based cloning tool for one-step generation of large mutant libraries - by Rosan Kuin academic.oup.com/bioinformatics…

Science has long relied on single ML models - powerful, but limited because they are bound by baked-in knowledge. Our recent experiments show that genuine discovery emerges when a very large number of agents interact, adapt, and co-create, much like biology itself. Last week at Harvard’s Big Data 2025 I shared how multi-agent swarms may allow us to move beyond pattern-analysis to invent - exemplified in very difficult problem spaces such as de novo proteins and music with long-range form. The swarms are formulated like reinforcement-learning collectives, where agents learn on the fly, adapt to each other, and evolve strategies in real time, to yield hallmarks of intelligence that a single model cannot exhibit. Our swarm generated proteins well outside natural and single-model clusters (UMAP), and the music scored the highest small-worldness with the most long-range links, the signature of integrated, human-like creative structure. In a deeper analysis, when we mapped how themes in the music connect across time, the swarm built networks with the tightest balance of local clusters and global connections, beating all baselines. The resulting composition was not just repeating patterns stitched together, but featured organic global coherence without repetition, like sparks of creativity emerging on their own. Preprints coming soon!

We are hiring! Come join our team. We still have GPUs and cake, but also very intelligent and motivated students..! This is a 2-year position in the area of computational drug discovery. universiteitleiden.nl/vacatures/2025…

Very happy to continue with this amazing project! rijksoverheid.nl/actueel/nieuws…

Integrating Pharmacokinetics and Quantitative Systems Pharmacology Approaches in Generative Drug Design pubs.acs.org/doi/10.1021/ac… @GJPvWesten @CDDLeiden #JCIM Vol65 Issue10 #MachineLearning #DeepLearning

Linde talking about her work at the #ICCS2025. Preprint here: chemrxiv.org/engage/chemrxi…

Counting down to the ICCS...! Oral presentation program online: iccs-nl.org/general-inform… Poster session online: iccs-nl.org/posters/ Last minute information and instructions: iccs-nl.org/instructions-f… Looking forward to a great conference!

The latest from CDD Leiden: Integrating Pharmacokinetics and Quantitative Systems Pharmacology Approaches in Generative Drug Design by Helle vd Maagdenberg pubs.acs.org/doi/10.1021/ac…

We are happy to inform you that we have drafted the preliminary program for the 13th ICCS. We were overwhelmed by the number and quality of the abstracts! We are happy to inform you that we could increase the max participants by 20 after discussing with the hotel! Submitters of an accepted abstract will be contacted ASAP by our conference office. For you the registration will open (under early bird rate) until May 2nd. Please respond and register ASAP. After May 2nd the general registration will open until May 25th. We are in talks with the hotel to see if we can also increase the total poster places by 10. We will update you asap. If you receive an 'on hold' response, please keep an eye on your inbox for an update. Note also that if an abstract was submitted twice (as oral and poster with separate IDs) one was rejected, and the other assessed on merit for oral and poster. @intconfchemstr

Paper Alert! 🔬 We tackled synthesizable de novo drug design using only in-house resources (~6,000 building blocks) and experimentally evaluated 3 MGLL inhibitor candidates, with one showing evident activity! rdcu.be/efMN5 #DrugDiscovery #GenAI #DeNovoDrugDesign #CASP

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/chemrxi…

We are very happy to confirm sponship of the ICCS by: @CCG_MOE (Premier sponsor) @chemaxon (Platinum sponsor) @cressetgroup (Silver sponsor) Thank you very much for the support of our great conference! See our website for more details: iccs-nl.org/sponsors/

RT @GJPvWesten: ! Deadline extended ! Dear community, We were informed that there were some issues with the website of the ICCS about a w…