Gabriel Ortega
@gabolab.bsky.social
Research lab at CIC bioGUNE (Bilbao, Spain). Biosensors, biomolecular engineering and protein biophysics. www.cicbiogune.es/people/gortega
Thanks also to others in the lab who helped out along the way. Link to bioRxiv paper: www.biorxiv.org/content/10.6...
De novo design of small-molecule-induced conformational change
Many biological proteins function by changing shape upon small-molecule binding. Here, we present a general strategy for designing de novo proteins that undergo small-molecule-induced conformational c...
biorxiv.org
This is a fantastic work, very powerful implications for biomolecular design and biosensing aplications!
Nick Polizzi@nickpolizzi.bsky.social · 21h agoWe can design "static" binders routinely now, but design of "dynamic" shape-changing proteins has remained quite hard. Jeffrey Chang and I asked: why can't we couple small-molecule binding to shape change? After all, natural proteins do it every day. In a new preprint, we show how it can be done. 🧵
1st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...
Complete Mutagenesis of the Genome and Proteome of ΦX174
The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge...
biorxiv.org
AI Raygun for shrinking proteins! Very nice work by @rohitsingh8080.bsky.social The naming is cool, but I also found concept of mimicking Natural protein evolution (insertions, deletions, mutations) very elegant. www.nature.com/articles/s41...
Miniaturizing and modifying natural proteins with Raygun - Nature
Probabilistic sequence encoding from language model embeddings within a generative AI framework enables protein miniaturization, modification and augmentation while maintaining native architectur...
nature.com
Rudolph A. “Rudy” Marcus, a Canadian-born US chemist whose work on electron transfer helped shape the entire field of chemistry, died on July 16 at age 102. He was a chemist at the California Institute of Technology and a Nobel laureate: cen.acs.org/people/obitu... #chemsky 🧪
#bioGUNE_Seminars | 🔬 Thanks to Benjamí Oller IQS for his seminar at #CICbioGUNE Basque Research and Technology Alliance - BRTA about how VEGF about engineering conditionally active protein therapeutics and brain-delivery strategies for neurological diseases 📅 https://www.cicbiogune.es/activities
Nature research paper: Zero-shot design of drug-binding proteins via neural iterative selection−expansion go.nature.com/4eZ6yeW
Zero-shot design of drug-binding proteins via neural iterative selection−expansion - Nature
By pairing two neural networks in an iterative optimization algorithm, small-molecule binding proteins can be designed from scratch with high accuracy, affinity and success rates, showing promise for applications in drug delivery and sequestration.
go.nature.com
Publicly available dataset of protein-ligand affinities and structures! In the era of AI models, high quality data is the key!
OpenBind@openbind.bsky.social · 3mo ago#OpenBind announces its first data drop marking a major milestone for AI‑Enabled #DrugDiscovery! It’s the first initiative to generate open, AI‑ready datasets for protein–drug complexes, produced continuously & at industrial scale to enable the next generation of #AI models. https://loom.ly/eIrsqqg
🔬 Biophysics Week a la @uvic-ucc.cat! El 25/03/26 acollim la xerrada “Nanorobots in action” amb la Dra. Maria Guix Noguera, per descobrir com la biofísica nano pot transformar la medicina del futur. 📍 Aula Magna 🕥 11:30 h 🔗 Inscripcions: tuit.cat/NgpwL #BioPhyzza2026 #BiophysicsWeek #UVicUCC #FCTE
🚨 𝐑𝐞𝐬𝐞𝐚𝐫𝐜𝐡 𝐇𝐢𝐠𝐡𝐥𝐢𝐠𝐡𝐭 🚨 💡epiGPTope: A Machine Learning-Based Epitope Generator and Classifier 📄 ACS Synthetic Biology 👉https://doi.org/10.1021/acssynbio.5c00693
In a development that could transform how scientists study cancer, neurodegeneration and inflammation, #UCSB researchers have invented a modular, genetically encoded, protein-based sensor that enables MRI machines to visualize molecular activity inside cells. Full story: https://ow.ly/cRmg50YqsiU
UCSB researchers develop a genetic sensor that could allow MRIs to image molecular-level changes
In a development that could transform how scientists study cancer, neurodegeneration and inflammation, researchers have invented a modular, genetically encoded, protein-based sensor that enables MRI machines to visualize molecular activity inside cells.
ow.ly
Oh no... 😢 se va uno de los mejores blogs que recuerdo. No sólo divulgaban sobre economía y políticas públicas, también representaban una forma de afrontar el debate racional, sosegada, humilde frente a la complejidad. Una víctima más de la inmediatez y la polarización de las redes sociales.
Nada es Gratis@nadaesgratis.bsky.social · 5mo agoCese de actividad del blog NeG vía @nadaesgratis.bsky.social #Economía nadaesgratis.es/editores/ces...
A detailed comparison of de novo designed proteins by NMR finally puts to rest the idea that structure prediction confidence metrics have any correlation with local flexibility
AI x Bio Discovery@aixbiobot.bsky.social · 6mo agoLarge-scale exploration of protein space by automated NMR [new] enables high-throughput experimental characterization of designed protein structure and dynamics, revealing how sequences encode motion.
Finding one mutation that improves a protein is hard. Finding five that work together is exponentially harder. Today in @science.org, Hsu and Konermann labs present MULTI-evolve, a lab-in-the-loop framework that does it in just one machine learning-guided round.
“It’s a major advance, on the scale of an AlphaFold4. The problem, of course, is that we know nothing of the details.” Isomorphic Lab’s proprietary drug-discovery model is a major advance go.nature.com/3Mm2ZnQ
‘An AlphaFold 4’ – scientists marvel at DeepMind drug spin-off’s exclusive new AI
Isomorphic Lab’s proprietary drug-discovery model is a major advance, but scientists developing open-source tools are left guessing how to achieve similar results.
go.nature.com
#bioGUNE_News | 🎉 Yesterday we celebrated our 21st anniversary at #CICbioGUNE @brtaeus.bsky.social with a cutting-edge scientific day 🔸 Isabel Fariñas on neural stem cell quiescence 🔸 June Ereño-Orbea on Siglec–sialoglycan cancer immunotherapy 🔗 www.cicbiogune.es/news/cic-bio...
My reply to @anshulkundaje.bsky.social on the other site has been quoted in this @nature.com report on Isomorphic's new DDE model, which relies on private data to a degree that is probably unprecedented in the history of this field 🧪🧬
Nature@nature.com · 6mo ago“It’s a major advance, on the scale of an AlphaFold4. The problem, of course, is that we know nothing of the details.” Isomorphic Lab’s proprietary drug-discovery model is a major advance go.nature.com/3Mm2ZnQ
Papers are like buses... You wait for ages, then two come along at once. Huge congrats to @bornanovak.bsky.social and @jefflotthammer.bsky.social for pushing and driving every aspect of this work, preprinted ~1 year ago to the day (Friday before BPS), now published! www.nature.com/articles/s41...
Accurate predictions of disordered protein ensembles with STARLING - Nature
The deep learning model STARLING can generate accurate ensembles of intrinsically disordered regions of proteins using only protein sequence as input.
nature.com
Borna Novak@bornanovak.bsky.social · last yr.Excited to announce the newest member of the flock - STARLING (conSTruction of intrinsicAlly disoRdered proteins ensembles efficientLy vIa multi-dimeNsional Generative models). www.biorxiv.org/content/10.1...
How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller? Excited to share our latest work in @science.org on a new small polymerase. 1/n
A small polymerase ribozyme that can synthesize itself and its complementary strand
The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...
science.org
Pleased to share the final version of this behemoth of a paper, now finally published. I guess I can retire now? www.nature.com/articles/s41... More functional data, many thousands of words removed, and a few other updates from last year's preprint.
Sequence and chemical specificity define the functional landscape of intrinsically disordered regions - Nature Cell Biology
Langstein-Skora, Schmid, Huth et al. propose that intrinsically disordered region functionality can be driven by the interplay between linear binding motifs and contextual chemical characteristics suc...
nature.com
Alex Holehouse@alexholehouse.bsky.social · 2y agoWe’re pleased to share our substantially updated (more below on that…) version of our manuscript exploring the relationship between conservation in sequence/function for intrinsically disordered regions (IDRs) www.biorxiv.org/content/10.1...
Like, look at this wonderful hand drawn structures! www.quantamagazine.org/how-colorful...
How Colorful Ribbon Diagrams Became the Face of Proteins | Quanta Magazine
Proteins are often visualized as cascades of curled ribbons and twisted strings, which both reveal and conceal the mess of atoms that make up these impossibly complex molecules.
quantamagazine.org
Gabriel Ortega@gabolab.bsky.social · 6mo agoIf you work with proteins, make sure to show your students Jane Richardson’s early drawings and sketches of protein structures. Not only because they are the foundation of virtually all protein representations today, but also because they are just beautiful!
If you work with proteins, make sure to show your students Jane Richardson’s early drawings and sketches of protein structures. Not only because they are the foundation of virtually all protein representations today, but also because they are just beautiful!
Frances Separovic@francesbiophys.bsky.social · 6mo agoStories from #WomenInScience who changed how we visualize #proteins: Ahead of her 85th birthday, Jane Richardson (Duke Univ, @biophysicalsoc.bsky.social president 2012-13) discussed her life from making a telescope to developing ribbon diagrams for 3D protein structure www.nature.com/articles/s41...
Stories from #WomenInScience who changed how we visualize #proteins: Ahead of her 85th birthday, Jane Richardson (Duke Univ, @biophysicalsoc.bsky.social president 2012-13) discussed her life from making a telescope to developing ribbon diagrams for 3D protein structure www.nature.com/articles/s41...
Stories from the scientist who changed how we visualize proteins - Nature Reviews Chemistry
Ahead of her 85th birthday, Jane Richardson, Professor of Biochemistry at Duke University, discussed her life in science from making her own telescope to developing the ribbon diagrams for the 3D stru...
nature.com
As scientists, we always hope to do something meaningful that improves people’s lives. @kwplaxco.bsky.social is achieving just that. Very exciting to see aptamer sensors moving one step closer to patients, and proud to have contributed my (little) grain of sand!
C&EN (Chemical & Engineering News)@cenmag.bsky.social · 6mo agoA wearable DNA-based sensor similar to a continuous glucose monitor can accurately and safely detect vancomycin concentrations in the body: cen.acs.org/analytical-c... #chemsky 🧪
Wavelength AND lifetime multiplexed imaging, cool! By @ciqus.bsky.social onlinelibrary.wiley.com/doi/full/10....
onlinelibrary.wiley.com
Very interesting study on the cardiac toxicity of doxorubicin chemotherapy. By researchers from CNIC, Spain: academic.oup.com/eurheartj/ad...
Anthracycline cardiotoxicity: role of metabolic vulnerability induced by cardiac pressure overload
AbstractBackground and Aims. Hypertension and valvular heart disease, both associated with left ventricular (LV) pressure overload, increase the risk of an
academic.oup.com
New preprint🚨 Imagine (re)designing a protein via inverse folding. AF2 predicts the designed sequence to a structure with pLDDT 94 & you get 1.8 Å RMSD to the input. Perfect design? What if I told u that the structure has 4 solvent-exposed Trp and 3 Pro where a Gly should be? Why to be wary🧵👇
