Biologist that navigates in the oceans of diversity through the space-time | MSc in Biochem/Bioinfo @ibt_unam πŸ‡²πŸ‡½ | Protein evo, metagenomics & AI/ML/DL

Mexico
Joined November 2020
1/12🧡Do you want to learn how to design proteins using AI but don’t know anything about bio? I created a free 10-lesson course on YouTube. It’s now available in Spanish (original) and English (autodubbing w/Kokoro 82M). Here’s an overview of the topics covered in each lecture :)
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
New de novo design model from Baker Lab + NVIDIA, available on Tamarind today. We are excited to be working with @NVIDIAHealth to bring access to RFD4-Proteina on day 0.
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
1/n Crossover episode! We introduce RFD4-Proteina, our latest design model - and the result of a year-long collaboration between the Baker Lab and NVIDIA GenAIR (the name says it all…). I hope you’ll agree - the results are astonishing. 🌐 Website: rfd4-proteina.org/
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
Avengers assemble: 1 year BakerLab + NVIDIA GenAIR = πŸ”₯ rfd4-proteina.org Presenting RFD4-Proteina, our latest protein design model, significantly better and faster than everything we compared against, both in silico and in the lab! 1/30
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
Public preview of BioEmu2! @MSFTResearch AI for Science’s new foundation model for biomolecular structure, dynamics and function. Open weights, MIT license. github.com/microsoft/bioemu2 Movie: BioEmu2-simulated binding of intrinsically disordered peptide PUMA to MCL-1 receptor. πŸ§΅β¬‡οΈ
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
We’re excited to share our new perspective in @MolecularCell on designing programmable biological behavior! (1/3) doi.org/10.1016/j.molcel.202…
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
🚨 RFdiffusion3 is officially published in Science! From the Baker lab, this next-generation AI model enables atom-level biomolecular design, going beyond protein structures to engineer complex catalytic sites. Experimentally validated results include de novo enzymes that degrade organophosphates and cleave disease-related peptides. πŸ“„ doi.org/10.1126/science.aeh2…
πŸ€– Made with AI
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
Coin labs is announcing our new decision model Flip-1. - Distilled down to 1 parameter - 50% on yes/no bench - Runs fully offline
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
Our paper is out in Nature Communications! We explore how viruses and encapsulins may have evolved from one another, with implications for the evolution of biological compartmentalization. Really happy to share this work! Thanks to all my coauthors! nature.com/articles/s41467-0…
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
Are you a PhD student interested in the intersection of machine learning and biology or healthcare? Come do an internship with the BioML Group at MSR! Make sure you submit a research statement! apply.careers.microsoft.com/…
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
A visualization of the different effort levels for Claude models. I find myself using medium for 80% of the tasks, high for ~15%, and occasionally will reach for xhigh or max when working on something super complex, but Opus 5.5 on medium I find perfect for most coding work.
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
terry tao: imagine, if you will, a petrifying situation. you have produced a very effective drug, but you do not know how it works. do you trust the drug? now, this is just a hypothetical, butβ€” drug developers:
This is a slide from Terence Tao's 'Math 2.0' public lecture yesterday evening at Caltech. I am highly confident that, if the cure actually worked, almost any Stage 4 cancer patient would tell you that human comprehension of its mechanism is completely irrelevant to them.
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
A universal predictive model of the cell would dramatically accelerate science, allowing biologists to perform experiments digitally. Today we’re announcing a major partnership with the DOE and NIH. The goal of this partnership is to generate the data that will be needed to build an accurate model of the cell with artificial intelligence. Isomorphic, Google DeepMind, and Meta are joining us as founding partners in the Virtual Biology Initiative. This is the beginning of a large scale coordinated effort to map cellular biology to power the development of digital models of life. Other leading scientific institutions and consortia including the Allen Institute, Broad Institute, Gladstone Institutes, the Human Cell Atlas, the Human Protein Atlas, the Wellcome Sanger Institute, as well as NVIDIA, are working together as part of this international scientific project. Creating a predictive model of the cell is one of the most important challenges for the next decade of science. The insights that come from this could unlock a far greater understanding of disease, and open new paths for cures. We invite the worldwide scientific community and other funders to join us in this effort.
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
Google DeepMind just moved protein AI from reading structures to designing chemistry. Its new system, AlphaProtein Novo, generates de novo enzymes for catalytic reactions β€” including enzymes that can synthesize drug-like piperidines and degrade the plasticizer DEHP, even at 90Β°C. The bigger story: AlphaFold learned to read proteins. AlphaProteo learned to design binders. Now AlphaProtein Novo is beginning to design catalysts. From predicting biology β†’ writing proteins β†’ engineering chemistry. Preprints and code: biorxiv.org/content/10.64898… biorxiv.org/content/10.64898… github.com/google-deepmind/a…
Introducing AlphaProtein Novo, a pipeline for de novo enzyme design! In collaboration with @francesarnold's group, we developed AP Novo and used it to get SoTA "novel-scaffold" activity on 2 benchmark reactions and create enzymes to synthesize the pharmaceutical motif piperidine and degrade the environmental toxin DEHP. Work led by @ZvxyWu @ZiqiLi0513 with teammates @alexechu_ @kelly_ruijie @schulluc @jacobjinkelly @rosaliags @davidla @solserpens @j_reisenbauer, @pengliu_group, Josh, Thomas, Amy, Tristan, Harshnira, and others. It was a joy and privilege to work with you all! Preprints and code: biorxiv.org/content/10.64898… biorxiv.org/content/10.64898… github.com/google-deepmind/a…
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
How do bacteria build their flagella? We’ve put together an animation of Salmonella flagellum assembly based on cryo-EM and X-ray structures. From the membrane-embedded machinery to the growing filament, here’s how the parts come together, step-by-step.
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
Good afternoon, San Francisco! Today, we're releasing Test-Time Structure-Space Search, a new OpenDDE inference algorithm for more effective co-folding when designing and selecting antibody drug candidates 🧬. 16% β†’ 78%, that's top-1 success on antibody–antigen targets where OpenDDE usually fails, using Test-Time Structure-Space Search with just five correct contacts. Frozen model. No retraining. No gradients through the network. Test-time compute isn't only for LLMs. Rather than only picking the best of many samples, we search for better structures while the sampler is still denoising. Same OpenDDE, same five contacts, same budget of 25 candidates per target: β€’ re-rank with the contacts: 33% β€’ steer the sampling with them: 78% Re-ranking recovers only about a quarter of the gain. The rest comes from changing the sampling trajectory itself. How it works: β€’ At scheduled denoising steps (about three dozen per sample), we check OpenDDE's predicted clean complex against the contacts. β€’ If they fail, a solver moves the antibody as a rigid body: Refine (nudge locally) β†’ Search (broad pose search, only if still failing) β†’ Refine (polish the best pose). β€’ A clash-aware energy refuses moves that create severe overlaps, and fused GPU kernels make thousands of pose evaluations per call practical. β€’ The corrected structure goes back to the sampler. If the contacts already hold, nothing moves. Results: 805 held-out SAbDab targets where the base model usually fails (median DockQ < 0.23 over five samples). Top-1 success by number of known contacts: 0 (unguided): 16% and 5: 78%. With 5 contacts, mean top-1 DockQ goes 0.14 β†’ 0.43 and the CAPRI-medium rate 11% β†’ 39%. Pocket mode (5 epitope residues, nothing on the antibody side): 17% β†’ 33%, versus 26% for re-ranking. A smaller gain, same pattern. Try it: Put contact pairs or epitope residues in the "constraint" field of your input JSON and run with --use_tfg_guidance true. Checkpoints and output format are unchanged, and inputs without a constraint behave as before. With the optional trunk cache, inputs that differ only in their constraint share one trunk. Examples for Fab, Fv and VHH are in examples/tfg. Fine print: Constraints are simulated from reference structures, so they are correct by construction. This measures what accurate interface knowledge is worth, not robustness to experimental noise, and wrong contacts can push success below unguided. SAbDab only. Success = DockQ β‰₯ 0.23, 25 candidates per target, 95% bootstrap CIs. Validated on one GPU with 200 diffusion steps. Code: github.com/aurekaresearch/Op… Tech Report: github.com/aurekaresearch/Op…
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
Replying to @claudeai
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GAMA Miguel Angel πŸ¦β€β¬›πŸ”‘ retweeted
The Institute for Protein Design is hiring postdocs! 🧬 We design new proteins to tackle big challenges in medicine, sustainability & technology. Interested in joining our interdisciplinary environment? Learn more here: ipd.uw.edu/join-us/
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