Reposted by Chris de GraafChris de Graaf @cdg-gpcr.bsky.social · 02/07/2025Closing the loop on #GenAI for #GPCR #SBDD www.nature.com/articles/s41... tinyurl.com/yeyhfr7jnature.comIdentification of nanomolar adenosine A2A receptor ligands using reinforcement learning and structure-based drug design - Nature CommunicationsHere 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... 1177
Chris de Graaf @cdg-gpcr.bsky.social · 02/07/2025Closing the loop on #GenAI for #GPCR #SBDD www.nature.com/articles/s41... tinyurl.com/yeyhfr7jnature.comIdentification of nanomolar adenosine A2A receptor ligands using reinforcement learning and structure-based drug design - Nature CommunicationsHere 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... 1177
Reposted by Chris de GraafDerek Lowe @dereklowe.bsky.social · 12/02/2025Biopharma 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.orgStand Up And Be Counted 17384158
Reposted by Chris de GraafDiego del Alamo @delalamo.xyz · 19/01/2025Protein 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... 28616
Reposted by Chris de GraafGerard JP van Westen @gjpvwesten.bsky.social · 17/01/2025If 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
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.comStructural and functional determination of peptide versus small molecule ligand binding at the apelin receptor - Nature CommunicationsThis 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... 020
Reposted by Chris de GraafChris de Graaf @cdg-gpcr.bsky.social · 15/12/2024@baoilleach.bsky.social on #Bluesky! 012
Reposted by Chris de GraafNature Portfolio @natureportfolio.nature.com · 13/12/2024Analysis 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 🧪 🏺 17613
Reposted by Chris de GraafPat Walters @wpwalters.bsky.social · 12/12/2024ChEMBL 35 is out. Happy Holidays! chembl.blogspot.com/2024/12/here...chembl.blogspot.comHere'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... 0275
Chris de Graaf @cdg-gpcr.bsky.social · 09/12/2024Reply 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.comMore 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... 000
Reposted by Chris de GraafMarwin Segler @marwinsegler.bsky.social · 09/12/2024new 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/2412.05269arxiv.orgChimera: Accurate retrosynthesis prediction by ensembling models with diverse inductive biasesPlanning 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... 48328
Reposted by Chris de GraafAlt National Park Service @altnps.bsky.social · 07/12/2024We keep getting messages saying climate change is a hoax and the world is flat. Is it 2024?! 444349545755
Reposted by Chris de GraafChris de Graaf @cdg-gpcr.bsky.social · 23/11/2024Moving #CADD #AI for #GPCR #SBDD posts and discussions to #Bluesky ! bsky.app/profile/cdg-... 061
Reposted by Chris de GraafChris de Graaf @cdg-gpcr.bsky.social · 23/11/2024Comparative Ligandability Analysis and new Nomenclature Allosteric GPCR binding sites pubs.acs.org/doi/10.1021/... tinyurl.com/ybthux9c #GPCR #CADD #SBDD #ALLODDpubs.acs.orgComparative Study of Allosteric GPCR Binding Sites and Their Ligandability PotentialThe 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... 2102
Reposted by Chris de GraafChris de Graaf @cdg-gpcr.bsky.social · 23/11/2024Closing 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 #SBDDchemrxiv.orgModern hit-finding with structure-guided de novo design: identification of novel nanomolar adenosine A2A receptor ligands using reinforcement learningGenerative 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... 041
Reposted by Chris de GraafPolaris @polarishub.io · 25/11/2024The 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/... 1137
Reposted by Chris de GraafTorsten 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.orgHome - CASP16 14016
Reposted by Chris de GraafChris de Graaf @cdg-gpcr.bsky.social · 28/11/2024More generally (not for HIV protease case specifically) I would propose to consider 4-5 options: 051
Reposted by Chris de GraafChris de Graaf @cdg-gpcr.bsky.social · 28/11/20241) Displace Energetically unfavorable water in lipophilic region with lipophilic ligand moiety 101
Reposted by Chris de GraafChris de Graaf @cdg-gpcr.bsky.social · 28/11/20242) Stabilise Design favorable ligand-water-protein mediated interaction by introduction polar ligand moiety 001
Reposted by Chris de GraafChris de Graaf @cdg-gpcr.bsky.social · 28/11/20243) Replace Polar ligand moiety mimicking energetically favorable water molecule 001
Reposted by Chris de GraafChris de Graaf @cdg-gpcr.bsky.social · 28/11/20244) Leave alone a) Energetically favorable molecule b) Bulk water/accessible region / no need to expand ligand in this direction unless for eg solubilising groups 001
Reposted by Chris de GraafChris de Graaf @cdg-gpcr.bsky.social · 28/11/20244-5 options/scenarios/sttategies how to deal with water in #SBDD #CADD #MedChem ? @darrylbmcconnell.bsky.social 011
Reposted by Chris de GraafCompound Interest | Chemistry infographics @compoundchem.com · 28/11/2024Happy Thanksgiving to those celebrating! Here's some relevant chemistry for the day: www.compoundchem.com/2017/11/23/t... #ChemSky 🧪 010034
Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024Thanks 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'). 100
Chris de Graaf @cdg-gpcr.bsky.social · 28/11/20244-5 options/scenarios/sttategies how to deal with water in #SBDD #CADD #MedChem ? @darrylbmcconnell.bsky.social 011
Chris de Graaf @cdg-gpcr.bsky.social · 28/11/20244) Leave alone a) Energetically favorable molecule b) Bulk water/accessible region / no need to expand ligand in this direction unless for eg solubilising groups 001
Chris de Graaf @cdg-gpcr.bsky.social · 28/11/20243) Replace Polar ligand moiety mimicking energetically favorable water molecule 001
Chris de Graaf @cdg-gpcr.bsky.social · 28/11/20242) Stabilise Design favorable ligand-water-protein mediated interaction by introduction polar ligand moiety 001
Chris de Graaf @cdg-gpcr.bsky.social · 28/11/20241) Displace Energetically unfavorable water in lipophilic region with lipophilic ligand moiety 101
Chris de Graaf @cdg-gpcr.bsky.social · 28/11/2024More generally (not for HIV protease case specifically) I would propose to consider 4-5 options: 051
Reposted by Chris de GraafDarryl B McConnell @darrylbmcconnell.bsky.social · 28/11/2024What 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? 183
Reposted by Chris de GraafWoody Sherman @woody-sherman.bsky.social · 26/11/2024Just 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.org2025 Computer Aided Drug Design Conference GRCThe 2025 Gordon Research Conference on Computer Aided Drug Design will be held in Portland, Maine. Apply today to reserve your spot. 25213
Reposted by Chris de GraafAltmetric @altmetric.com · 18/11/2024We 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 #Altmetricsdocs.bsky.appAction Intent Links | BlueskyAuthors, 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... 166113164572
Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024Moving #CADD #AI for #GPCR #SBDD posts and discussions to #Bluesky ! bsky.app/profile/cdg-... 061
Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024Looking 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 #SBDDgpcrs-europe.comExpert Speaker Faculty | GPCRs-Targeted Drug Discovery Summit EuropeView our world-class speaker faculty at the GPCRs-Targeted Drug Discovery Summit Europe | 26-28 November, London, UK. 000
Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024Closing 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 #SBDDchemrxiv.orgModern hit-finding with structure-guided de novo design: identification of novel nanomolar adenosine A2A receptor ligands using reinforcement learningGenerative 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... 041
Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024Comparative Ligandability Analysis and new Nomenclature Allosteric GPCR binding sites pubs.acs.org/doi/10.1021/... tinyurl.com/ybthux9c #GPCR #CADD #SBDD #ALLODDpubs.acs.orgComparative Study of Allosteric GPCR Binding Sites and Their Ligandability PotentialThe 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... 2102
Chris de Graaf @cdg-gpcr.bsky.social · 23/11/2024Many thanks Cornelius for organising, can you add me to the assemble of GPCR aficionados? Thanks! 100
Reposted by Chris de GraafGreg Landrum @greglandrum.bsky.social · 22/10/2024Save 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. 05022
Reposted by Chris de GraafMarwin Segler @marwinsegler.bsky.social · 12/11/2024Interesting 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/dZWa9rdcu.beMolE: a foundation model for molecular graphs using disentangled attentionNature 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... 1325
Reposted by Chris de GraafSrijit Seal 🇺🇸🇬🇧🇩🇪🇯🇵🇮🇳 @srijitseal.com · 17/11/2024Here'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 317421