Thanks for featuring our work, @iwatobipen.bsky.social! @edgarlopez2.bsky.social @jose-difacquim.bsky.social

pen(Taka)@iwatobipen.bsky.social · 2mo ago

Try to use new fragmentation method of small molecules #cheminformatics #rdkit #crush As readers know that RECAP and BRICS are famous fragmentation method of molecules. Both methods use pre-defined rules. Today I found new fragmentaion method named CRUSH in Journal of cheminformatics reported from…

Our paper describing curation of bioactivity data for drugs and their associated metabolites is now published in Molecular Pharmaceutics. We were surprised to see that 26% of metabolites had either increased or retained activity compared to their parent drugs. Paper: pubs.acs.org/doi/10.1021/...

Our advanced molecular fragmentation algorithm CRUSH is now published in Journal of Cheminformatics. Check it out here: link.springer.com/article/10.1... with @edgarlopez2.bsky.social, @jose-difacquim.bsky.social

CRUSH—Cleavage Rules Using SMIRKS Heuristics: an enhanced molecular fragmentation algorithm - Journal of Cheminformatics

Molecular fragmentation methods are central to fragment-based discovery, virtual screening, and de novo molecular design, yet most existing approaches remain constrained by classical retrosynthetic ru...

link.springer.com

Excited to share our pre-print on the curation of a new bioactivity dataset for metabolic transformations. 🧪🧑‍💻 We were surprised to find that roughly a quarter of our drug-metabolite-target combinations contain metabolites with retained or increased bioactivity relative to the parent drugs! #chemsky

Work led by industrial PhD student Sofia Larsson and in close collaboration with Susanne Winiwarter and @filipmiljkovic.bsky.social at AstraZeneca. 📄 Paper: chemrxiv.org/doi/full/10.... 💻 Code: github.com/tsofiac/drug... 💽 Data: zenodo.org/records/1874...

The Issue “Good Practices in AI: Democratization of Open Science” is out. Honored to serve as Guest Editor and work with outstanding colleagues @filipmiljkovic.bsky.social @rociomer.bsky.social @wpwalters.bsky.social 👉 www.sciencedirect.com/special-issu... #AI #OpenScience #Chemoinformatics

Excited to share our recent paper, ”Compressing Biology,” to be presented at the Imageomics workshop at NeurIPS 2025. 🔬💻 Work led by my amazing PhD student Télio Cropsal. #cellpainting #stablediffusion #imageomics arxiv.org/abs/2510.19887

Compressing Biology: Evaluating the Stable Diffusion VAE for Phenotypic Drug Discovery

High-throughput phenotypic screens generate vast microscopy image datasets that push the limits of generative models due to their large dimensionality. Despite the growing popularity of general-purpos...

arxiv.org

And Part II of our Metabolite Identification (MetID) Data in Drug Discovery is out: pubs.acs.org/doi/10.1021/... Here we explore application of MetID proprietary data to expand the capacity of site-of-metabolism (SoM) #ML models. The paper and SoM data are both #openacess. #Zenodo #ADME

Metabolite Identification Data in Drug Discovery, Part 2: Site-of-Metabolism Annotation, Analysis, and Exploration for Machine Learning

The ability to pinpoint and predict sites of metabolism (SoMs) is essential for designing and optimizing effective and safe bioactive small molecules. However, the number of molecules with annotated S...

pubs.acs.org

Our paper on metabolite identification (MetID) data generation and trend analysis is now live and #openacess in Mol. Pharmaceutics @acs.org. In addition, we share proprietary MetID schemes for 120 compounds on #Zenodo. Link: pubs.acs.org/doi/10.1021/... Stay tuned for Part II! #dmpk #openscience

Metabolite Identification Data in Drug Discovery, Part 1: Data Generation and Trend Analysis

In drug discovery, metabolite identification data are used to identify metabolic soft spots in research molecules to facilitate reduced metabolism in subsequently designed compounds. In addition, know...

pubs.acs.org

Pleased to announce that our research on LAGOM, a transformer-based model for predicting chemical structures of potential drug metabolites, has been published in Artificial Intelligence in the Life Sciences. #compchem #chemsky

Rocío Mercado Oropeza@rociomer.bsky.social · 11mo ago

Excited to share that our paper "LAGOM: A transformer-based chemical language model for drug metabolite prediction" has been accepted in AILSCI! doi.org/10.1016/j.ai... Work led by Sofia Larsson and Miranda Carlsson, with @rbeckmann.bsky.social and Filip Miljković‬ (AZ)! #compchem #chemsky

Excited to share that our paper "LAGOM: A transformer-based chemical language model for drug metabolite prediction" has been accepted in AILSCI! doi.org/10.1016/j.ai... Work led by Sofia Larsson and Miranda Carlsson, with @rbeckmann.bsky.social and Filip Miljković‬ (AZ)! #compchem #chemsky