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Chris de Graaf

@cdg-gpcr.bsky.social
321 followers 307 following 21 posts

Head of Computational Drug Discovery and Data Science at Structure Therapeutics | GPCR | SBDD | CADD | Cheminformatics | Computational Chemistry | Medicinal Chemistry | Drug Design

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Reposted by Chris de Graaf
Chris de Graaf @cdg-gpcr.bsky.social · 02/07/2025
Closing the loop on #GenAI for #GPCR #SBDD www.nature.com/articles/s41... tinyurl.com/yeyhfr7j
nature.com
Identification of nanomolar adenosine A2A receptor ligands using reinforcement learning and structure-based drug design - Nature Communications
Here the authors combine a deep generative model with structure-based drug design and prospectively validate functionally active, nanomolar, A2A adenosine receptor ligands and solve their crystal stru...
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Chris de Graaf @cdg-gpcr.bsky.social · 02/07/2025
Closing the loop on #GenAI for #GPCR #SBDD www.nature.com/articles/s41... tinyurl.com/yeyhfr7j
nature.com
Identification of nanomolar adenosine A2A receptor ligands using reinforcement learning and structure-based drug design - Nature Communications
Here the authors combine a deep generative model with structure-based drug design and prospectively validate functionally active, nanomolar, A2A adenosine receptor ligands and solve their crystal stru...
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Reposted by Chris de Graaf
Derek Lowe @dereklowe.bsky.social · 12/02/2025
Biopharma companies and CEOs are keeping their heads down at their own peril. They should speak up about what’s happening to the NIH and other science agencies before it’s too late. Silence gives consent. And no one should consent to this.
science.org
Stand Up And Be Counted
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Reposted by Chris de Graaf
Diego del Alamo @delalamo.xyz · 19/01/2025
Protein backbone diffusion models consistently undersample catalytically important motifs, and oversample idealized helices, raising questions about the appropriateness of these methods in designing starting points for enzyme design & evolution. From www.biorxiv.org/content/10.1...
Protein structure embeddings reveal undersampled and de novo structure space. (B) First two principal components of mean-pooled ESM3 embeddings colored by helix content determined by DSSP. The indicated dashed guide lines denote visual boundaries of native structure space not sampled (Undersampled) and novel regions of protein structure for this space only observed in samples but not in native structures (De novo). (C) Rasterized visualization of panel B with 16 equally spaced grid squares in each principal component axis. A representative structure from each grid was chosen at random. Empty grid squares indicate the absence of any structure in the enclosed region. De novo alpha helices are shaded along the lower-right diagonal and the structures from CATH which do not have corresponding structures in the samples are shaded along the left and top rims. The structures are displayed in CATH raster plot are given in the Supplementary Information.
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Reposted by Chris de Graaf
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...
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Chris de Graaf @cdg-gpcr.bsky.social · 10/01/2025
Many thanks @gati.bsky.social!
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Chris de Graaf @cdg-gpcr.bsky.social · 10/01/2025
#StructuralBiology insights into #Genetic #GPCR variations identified in the UK 100,000 Genomes Project with differentiating effects on peptide (affected) vs. small molecule agonists (not affected) #pharmacology www.nature.com/articles/s41...
nature.com
Structural and functional determination of peptide versus small molecule ligand binding at the apelin receptor - Nature Communications
This study explores apelin receptor’s role in cardiovascular function, identifying residues critical for binding through genetic variants, AlphaFold2 modelling and base editing in cardiomyocytes. Co-c...
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Reposted by Chris de Graaf
Chris de Graaf @cdg-gpcr.bsky.social · 15/12/2024
@baoilleach.bsky.social on #Bluesky!
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Chris de Graaf @cdg-gpcr.bsky.social · 15/12/2024
@baoilleach.bsky.social on #Bluesky!
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Reposted by Chris de Graaf
Nature Portfolio @natureportfolio.nature.com · 13/12/2024
Analysis of the oldest-known genomes from early modern humans in Europe, who lived around 45,000 years ago, helps to provide a more precise date for when Neanderthals and modern humans mixed, according to research published in Nature. go.nature.com/3ZR8Kh1 🧪 🏺
This is figure 1, which shows the geographical distribution of modern human specimens older than 40 ky that produced genome wide data
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Reposted by Chris de Graaf
Pat Walters @wpwalters.bsky.social · 12/12/2024
ChEMBL 35 is out. Happy Holidays! chembl.blogspot.com/2024/12/here...
chembl.blogspot.com
Here's a nice Christmas gift - ChEMBL 35 is out!
Use your well-deserved Christmas holidays to spend time with your loved ones and explore the new release of ChEMBL 35!            This fresh...
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Chris de Graaf @cdg-gpcr.bsky.social · 09/12/2024
Reply by Jain and colleagues on the response of Corso and colleagues:. More response to the response (DiffDock/DiffDock-L) www.linkedin.com/pulse/more-r...
linkedin.com
More response to the response (DiffDock/DiffDock-L)
To amplify on what Pat Walters said (quotes from Gabriel Corso's post in italics): It only took a few days (in August 2023) for Ann Cleves, Pat, and me to figure out that the original DiffDock work ha...
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Reposted by Chris de Graaf
Marwin Segler @marwinsegler.bsky.social · 09/12/2024
new preprint on chemical synthesis ML models - showing how to combine multiple models in a principled way - modern Transformers + GNN to featurize chemical reaction: - new insights in where the models shine + bonus: find the quirky named reaction! Feedback welcome! arxiv.org/abs/2412.05269
arxiv.org
Chimera: Accurate retrosynthesis prediction by ensembling models with diverse inductive biases
Planning and conducting chemical syntheses remains a major bottleneck in the discovery of functional small molecules, and prevents fully leveraging generative AI for molecular inverse design. While ea...
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Alt National Park Service @altnps.bsky.social · 07/12/2024
We keep getting messages saying climate change is a hoax and the world is flat. Is it 2024?!
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Chris de Graaf @cdg-gpcr.bsky.social · 01/12/2024
Of: Alles voor zoete koek slikken
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John P. Overington @jpoverington.bsky.social · 27/11/2024
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Reposted by Chris de Graaf
Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024
Moving #CADD #AI for #GPCR #SBDD posts and discussions to #Bluesky ! bsky.app/profile/cdg-...
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Reposted by Chris de Graaf
Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024
Comparative Ligandability Analysis and new Nomenclature Allosteric GPCR binding sites pubs.acs.org/doi/10.1021/... tinyurl.com/ybthux9c #GPCR #CADD #SBDD #ALLODD
pubs.acs.org
Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential
The steadily growing number of experimental G-protein-coupled receptor (GPCR) structures has revealed diverse locations of allosteric modulation, and yet few drugs target them. This gap highlights the...
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Reposted by Chris de Graaf
Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024
Closing the CADD AI SBDD loop - From GPCR structures to RNN de novo drug design and back again! chemrxiv.org/engage/chemr... #GPCR #AI #RNN #CADD #SBDD
chemrxiv.org
Modern hit-finding with structure-guided de novo design: identification of novel nanomolar adenosine A2A receptor ligands using reinforcement learning
Generative chemical language models have demonstrated success in learning language-based molecular representations for de novo drug design. Here, we integrate structure-based drug design (SBDD) princi...
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Reposted by Chris de Graaf
Polaris @polarishub.io · 25/11/2024
The first paper from the Small Molecule Steering Committee at Polaris introduced practical guidelines for method comparison in ML-driven drug discovery. We'll be discussing this live on Dec 5th from 11 - 12 PM ET. Join the convo: portal.valencelabs.com/events/post/...
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Chris de Graaf @cdg-gpcr.bsky.social · 01/12/2024
Bijvoorbeeld: Koekje van eigen deeg
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Chris de Graaf @cdg-gpcr.bsky.social · 01/12/2024
🙋‍♂️👨‍💻
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Torsten Schwede @torstenschwede.bsky.social · 01/12/2024
#CASP16 results are online at the prediction center website - conference starting tomorrow evening. Have a safe trip - see you soon! predictioncenter.org/casp16/
predictioncenter.org
Home - CASP16
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Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
More generally (not for HIV protease case specifically) I would propose to consider 4-5 options:
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Reposted by Chris de Graaf
Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
1) Displace Energetically unfavorable water in lipophilic region with lipophilic ligand moiety
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Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
2) Stabilise Design favorable ligand-water-protein mediated interaction by introduction polar ligand moiety
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Reposted by Chris de Graaf
Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
3) Replace Polar ligand moiety mimicking energetically favorable water molecule
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Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
4) Leave alone a) Energetically favorable molecule b) Bulk water/accessible region / no need to expand ligand in this direction unless for eg solubilising groups
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Reposted by Chris de Graaf
Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
4-5 options/scenarios/sttategies how to deal with water in #SBDD #CADD #MedChem ? @darrylbmcconnell.bsky.social
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Reposted by Chris de Graaf
Compound Interest | Chemistry infographics @compoundchem.com · 28/11/2024
Happy Thanksgiving to those celebrating! Here's some relevant chemistry for the day: www.compoundchem.com/2017/11/23/t... #ChemSky 🧪
Infographic on the chemistry of turkey flavour. A huge number of chemical reactions occur when you stick your turkey in the oven, including the Maillard reaction, which occurs between amino acids and sugars in the meat during cooking.

Hundreds of products are formed by the Maillard reaction, including furans, furanones, pyrazines and thiophenes. Compounds called melanoidins are also formed, which contribute to the brown colouration that develops during cooking.
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Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
Thanks Darryl! I appreciate your choice of merging options from design strategy perspective - i.e. placement of groups in the location of the water - My proposal was to differentiate choice of: a) lipophilic ligand moiety (water 'displacement'), vs. b) 'polar' ligand moiety (water 'replacement').
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Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
4-5 options/scenarios/sttategies how to deal with water in #SBDD #CADD #MedChem ? @darrylbmcconnell.bsky.social
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Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
4) Leave alone a) Energetically favorable molecule b) Bulk water/accessible region / no need to expand ligand in this direction unless for eg solubilising groups
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Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
3) Replace Polar ligand moiety mimicking energetically favorable water molecule
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Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
2) Stabilise Design favorable ligand-water-protein mediated interaction by introduction polar ligand moiety
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Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
1) Displace Energetically unfavorable water in lipophilic region with lipophilic ligand moiety
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Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024
More generally (not for HIV protease case specifically) I would propose to consider 4-5 options:
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Reposted by Chris de Graaf
Darryl B McConnell @darrylbmcconnell.bsky.social · 28/11/2024
What to do with waters in drug discovery is one of the most important decisions that drug designers need to make. What would you do with the FLAP water on HIV protease? Address or Replace?
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Woody Sherman @woody-sherman.bsky.social · 26/11/2024
Just announced: 2025 Computer-Aided Drug Design (CADD) GRC program The topic: "Exploring the Synergy of Machine Learning and Physics-Based Computational Chemistry to Accelerate Drug Discovery" It is shaping up to be a seminal conference. Hope to see you there! www.grc.org/computer-aid...
grc.org
2025 Computer Aided Drug Design Conference GRC
The 2025 Gordon Research Conference on Computer Aided Drug Design will be held in Portland, Maine. Apply today to reserve your spot.
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Altmetric @altmetric.com · 18/11/2024
We strongly suggest that academic publishers and other platforms that host research rapidly implement a Share to Bluesky button for their articles. Here's how: docs.bsky.app/docs/advance... #AcademicSky #HigherEd #Altmetrics
docs.bsky.app
Action Intent Links | Bluesky
Authors, websites, and apps can use action intent links to implement "Share on Bluesky" buttons, or similar in-app actions. Logged-in users will be directed to the corresponding action view in the Blu...
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Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024
Moving #CADD #AI for #GPCR #SBDD posts and discussions to #Bluesky ! bsky.app/profile/cdg-...
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Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024
Looking forward to interacting with GPCR experts at the GPCRs-Targeted Drug Discovery Summit - incl. Allosteric GPCR Drug Discovery workshop and presenting on Customising CADD for SBDD Targeting the Elusive Ligand & Water Induced GPCR Pocketome gpcrs-europe.com/whats-on/spe... #GPCR #CADD #SBDD
gpcrs-europe.com
Expert Speaker Faculty | GPCRs-Targeted Drug Discovery Summit Europe
View our world-class speaker faculty at the GPCRs-Targeted Drug Discovery Summit Europe | 26-28 November, London, UK.
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Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024
Closing the CADD AI SBDD loop - From GPCR structures to RNN de novo drug design and back again! chemrxiv.org/engage/chemr... #GPCR #AI #RNN #CADD #SBDD
chemrxiv.org
Modern hit-finding with structure-guided de novo design: identification of novel nanomolar adenosine A2A receptor ligands using reinforcement learning
Generative chemical language models have demonstrated success in learning language-based molecular representations for de novo drug design. Here, we integrate structure-based drug design (SBDD) princi...
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Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024
Comparative Ligandability Analysis and new Nomenclature Allosteric GPCR binding sites pubs.acs.org/doi/10.1021/... tinyurl.com/ybthux9c #GPCR #CADD #SBDD #ALLODD
pubs.acs.org
Comparative Study of Allosteric GPCR Binding Sites and Their Ligandability Potential
The steadily growing number of experimental G-protein-coupled receptor (GPCR) structures has revealed diverse locations of allosteric modulation, and yet few drugs target them. This gap highlights the...
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Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024
Many thanks Cornelius for organising, can you add me to the assemble of GPCR aficionados? Thanks!
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Greg Landrum @greglandrum.bsky.social · 22/10/2024
Save the date: I'm happy to announce that the 2025 RDKit UGM will take place in Prague, Czechia from 10-12 September. The organizers are Martin Šícho and Daniel Svozil from the University of Chemistry and Technology in Prague. Registration details will follow early next year.
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Marwin Segler @marwinsegler.bsky.social · 12/11/2024
Interesting new paper on large scale small molecule model pre-training for property prediction by Recursion - pretraining in this domain isn’t necessarily as easy to get to work as in inages or language rdcu.be/dZWa9
rdcu.be
MolE: a foundation model for molecular graphs using disentangled attention
Nature Communications - Predictive models for chemistry are typically trained on small data sets, making it difficult to generalize well. Here, the authors describe a foundation model trained on...
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Chris de Graaf @cdg-gpcr.bsky.social · 22/11/2024
Thanks Marwin! Can you add me?
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Srijit Seal 🇺🇸🇬🇧🇩🇪🇯🇵🇮🇳 @srijitseal.com · 17/11/2024
Here's a Cheminformatics Starter pack! Let me know if you would like to be added! And more importantly, do encourage people to join the blue skies :D
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