Try to use nesso-1 for binding affinity prediction #cheminformatics #rdkit #folding ai Now there are lots of AI tools for drug discovery. I think it's difficult to expect 8 years before when I moved to cheminformatics team from MedChem 🙂 And one of the hot area is Folding AI such as Boltz, Alpha…

The Curvenote Reader button is live on bioRxiv! 😎 Click it to explore papers in a new way—zoom figures, pull up references without leaving the page. Button appears 48 hours after papers drop. Feedback? DM us or hit the GitHub repo. openrxivlabs.org/articles/rea...

Why we’re expanding the openRxiv Labs Curvenote Reader experiment

Read on for early results and what we’ll be looking at in the next phase.

openrxivlabs.org

🚨New PDBe webinar Bringing structural biology to AI: exploring the PDBe MCP servers The session will explore the capabilities offered by the PDBe MCP servers with practical examples. 🗓️ 9 September 2026 🕘 14:30-15:30 (BST) ⬇️ Register here ⬇️ www.ebi.ac.uk/training/eve... #PDB

Does the (live) shingles vaccine protect against dementia? Fergus Hamilton and colleagues provide important evidence in a new preprint using hospital data from the whole of England in a regression discontinuity design from which we *don't* show evidence of a meaningful protective effect /cont

I wrote about the completely wild incident where OpenAI were testing a new model and it broke out of its sandbox and broke INTO Hugging Face to steal the answers to the benchmark https://simonwillison.net/2026/Jul/22/openai-cyberattack/

Rules, for what can be a good drug, are extremely valuable in #DrugDiscovery. Nevertheless, it seems like once in a while all of these rules need to be thrown out of the window as exemplified by Nibrozetone that is investigated in Phase III for cancer treatment. drughunter.com/molecule/rrx...

nibrozetone

Nibrozetone (RRx-001), identified via a phenotypic screen of compounds from the rocket fuel industry, has been advanced by EpicentRx into multiple clinical trials. The molecule additionally received a...

drughunter.com

Function of a protein: something the protein does. Function in maths: a mapping from X to Y. Function in code: re-use code to do a task. Function at a conference: have a drink and look at posters.

Material for MkDocs 9.7.7 is out. It fixes a DOM-based XSS issue in the optional search.suggest feature, which was responsibly disclosed to us. Please update. Material for MkDocs will continue receiving security updates through November 5, 2026. github.com/squidfunk/mk...

Release mkdocs-material-9.7.7 · squidfunk/mkdocs-material

Warning Material for MkDocs is approaching end of life Material for MkDocs is scheduled to reach end of life on November 5, 2026. Until then, maintenance is limited to critical bug fixes and securi...

github.com

Nobel laureate Susumu Tonegawa, who pioneered cell-type-specific transgenic mice and the study of engrams, has passed away at the age of 86. By @claudia-lopez.bsky.social www.thetransmitter.org/memory/susum...

In memoriam: Susumu Tonegawa, ‘intellectual giant’

He won the Nobel Prize for his work on immunology and then went on to define the field of learning and memory.

thetransmitter.org

This Week In Cheminformatics Issue #030 is out. This week we look into How useful are Cavity Prediction Algorithms, NMR-AI, (Failing at) Predicting Alternative Binding Modes via Docking and a long list of papers. Happy reading :) thisweekincheminformatics.substack.com/p/thirty

This Week In Cheminformatics: Issue #030

How useful are Cavity Prediction Algorithms, NMR-AI, (Failing at) Predicting Alternative Binding Modes via Docking and a long list of papers...and maybe the last one of these from PT.

thisweekincheminformatics.substack.com

Guest Post — Why Research Expectations Have Outpaced the Systems That Enabled Them (Part 1) scholarlykitchen.sspnet.org/2026/07/20/g...

Guest Post — Why Research Expectations Have Outpaced the Systems That Enabled Them (Part 1) - The Scholarly Kitchen

Today's guest blogger questions the operating model around scholarly research and asks why these capabilities are so difficult to sustain at scale.

scholarlykitchen.sspnet.org

1/11 New preprint from the Sternberg lab in collaboration with the Fernández lab! We are excited to share our structure-function study of DRT10, a bacterial defense-associated reverse transcriptase that synthesizes long tandem-repeat DNA.🧵 Read the full story here: www.biorxiv.org/content/10.6...

Mechanism of tandem-repeat DNA synthesis by an antiviral reverse transcriptase

Defense-associated reverse transcriptases (DRTs) employ DNA synthesis to protect bacteria against phage infection[1][1],[2][2]. We previously showed that DRT10, a tripartite system comprising an RT, a...

biorxiv.org

PhyKIT v2.2.0 is out! PhyKIT has been rigorously profiled and optimized across the entire codebase, resulting in speedups ranging from ~1.0x to 16.6x, with a geometric mean of 2.0x Python 3.10 through 3.13 is also supported

Zensical Studio is out, and the bigger picture is coming together. We're building the next-generation Docs-as-Code stack, end to end, and we're right on track. More in tomorrow's newsletter. zensical.org/about/newsle...

Zensical@zensical.org · last mo.

Material for MkDocs proved the value of Python Markdown for technical writing. With Zensical, we’re now integrating the layers around it: parser, editor tooling, build, and publishing. We’ll share more in tomorrow’s newsletter. zensical.org/about/newsle...

The unparalleled productivity boost of the dual monitor set up!

Who benefits from Fast & Fair peer review? It benefits everybody. It benefits authors because they get a fast and high-quality review. It benefits editors because the editors handling the manuscripts don’t have to spend a lot of time finding reviewers.

Two weeks ago, our FlashPPI paper was published in @pnas.org. Today, we introduce our updated model, FlashPPI2. Fine-tuned on new AlphaFold structures, this new model achieves a 17% improvement over FlashPPI on the E. coli protein interaction benchmark. seqhub.org/blog/flashppi2

"Why paying peer reviewers works" Very cool initiative by @biologyopen.bsky.social and EiC Daniel Goerlick. Paying vetted(!) peer reviewers increased turnaround time & quality of #PeerReview! I continue to be a big fan of the Company of @biologists.bsky.social & their work. 👍 #SciPub

Why paying peer reviewers works, according to a journal’s editor-in-chief

A biology journal that paid peer reviewers found that the approach cut the time to a first editorial decision by 85% and maintained high-quality reviews.

nature.com

Our paper "Gene ancestries reveal diverse microbial associations during eukaryogenesis.” is finally out in Nature. Eukaryogenesis was likely a gradual process shaped by multiple microbial partners and virus-mediated gene transfer, rather than a single binary symbiosis. doi.org/10.1038/s415...

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites pubmed.ncbi.nlm.nih.gov/42376815/

Turning to Pandas chunking, Dask, and Polars, Jiayan Yin proposes several approaches for navigating memory bottlenecks in your data engineering pipelines.

What Can We Do When Memory Becomes the New Bottleneck in Data Engineering? | Towards Data Science

How Pandas chunking, Dask, and Polars help process millions of records when adding more compute isn't an option.

towardsdatascience.com

Lol, a paper that describes my life. My natural reaction to feeling like I'm finally getting the hang of something has always been to drop it and try something else. And somehow I still often feel like I'm not getting out fast enough.

How do we close the diagnostic gap for #Chagas disease? With only about 10% of people diagnosed and 1% receiving care, experts have defined priorities for better rapid & molecular diagnostics and improved access to care. doi.org/10.1186/s128... @bmc.springernature.com

Advancing diagnostics for Chagas disease: key product characteristics and harmonized evaluation strategies - an expert meeting report - BMC Infectious Diseases

Chagas disease is a global public health issue, life-threatening parasitic disease, affecting mostly underserved communities in Latin America. Yet, 10% of infected individuals are diagnosed, and 1% receive etiological treatment. Priority actions for disease elimination by 2030 are streamlining diagnostic methods and evaluating and developing point-of-care diagnostics. We convened 44 researchers, test developers, and health authorities, to provide scientific advice and reach consensus on (i) a harmonized protocol for evaluation of rapid diagnostic tests; (ii) preferred molecular diagnostics characteristics (scope, performance, operational features, pricing, and evaluation standards); and (iii) economic impact evidence needed to have a transformational impact in primary healthcare. We considered global and national perspectives with discordant evidence from multiple disciplines. Our outcomes provide a reference on practical applications and recommendations to promote test development and evaluation. Finally, we debate about the appropriate approach moving forward to meet the diagnostic gap, and propose how investments could be stimulated.

doi.org

Unreliable and underperforming antibodies are a longstanding problem, so while the reveal of apparently manipulated antibody data in Thermo Fisher's catalog was a shock, the frustration it sparked among many researchers is perhaps no surprise. My reporting:

Science sleuths uncover more than 100 suspicious images in Thermo Fisher antibody catalogue

Scientists have long worried about the reliability of commercial antibodies, and the latest findings have sparked fresh concerns.

nature.com

Proteins are the machinery of life. Billions of their sequences have been cataloged—but the biology behind most is still unknown. Today we're releasing ESMFold2, ESMC and ESM Atlas to help change that. Open source, open to every scientist. biohub.ai/esm/protein

Daraxonrasib is the first drug to substantially extend survival in pancreatic cancer trials. Median survival reached 13+ months compared to <7 months for chemo. It finally shuts down the "undruggable" KRAS protein, once called a greasy ball, using a novel molecular glue. #MedSky

How an ‘Impossible’ Idea Led to a Pancreatic Cancer Breakthrough

nytimes.com

Mannosylated nanoparticle immunogens enhance the circumsporozoite protein-specific B cell response and improve protection against sporozoite challenge https://www.biorxiv.org/content/10.64898/2026.05.04.722690v1

May is #MaintainerMonth! Meet the humans behind your favorite #RStats packages All month, we will spotlight the maintainers behind rOpenSci's software ecosystem. Stay tuned to meet them!

We built an AI that will tell you what will get your grant rejected. It’s a tough critique, but it’s better to know when you can still do something about it 👇 @qedscience.bsky.social

PDBe-SIFTS: an open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search https://www.biorxiv.org/content/10.64898/2026.04.30.721839v1