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Randy Read 🇨🇦🇬🇧

@randyjread.bsky.social

Interested in likelihood-based methods for structural biology. Contributor to Phenix, CCP4 and CCP-EM. Based at CIMR, University of Cambridge. Posts usually about science.

89 Posts1696 Follower169 Folgt
Alisia Fadini@alisiafadini.bsky.social · 2w ago

Atomic models powered bioAI's first era. Experiments measure more. @rs-station.bsky.social is joining omsf.io to unlock interpretation of raw exp observables at scale (blog👇); we'll partner with @openfold.io, @openbind.bsky.social , and cryo-EM+X-ray facilities to make this routine. Join us!

Open Molecular Software Foundation

Making bonds Building open source software and communities for the molecular sciences.

omsf.io

Reciprocal Space Station@rs-station.bsky.social · 2w ago

1/ We're excited to announce that @rs-station.bsky.social is joining the Open Molecular Software Foundation @omsf.io!

Briggs Group@briggsgroup.bsky.social · 3mo ago

The architecture of carriers formed by AP3:ARF1 for lysosomal membrane protein transport: www.science.org/doi/10.1126/.... Work from @jggkaufman.bsky.social, in collaboration with @dgershlick.bsky.social and David Owen. @mpibiochem.bsky.social @thecimr.bsky.social

Architecture of clathrin-independent AP3:ARF1-coated carriers

AP3 generates clathrin-free carriers on endosomes by organizing via ARF1 dimers into elongated membrane-deforming arrays.

science.org

Randy Read 🇨🇦🇬🇧@randyjread.bsky.social · 3mo ago

Yes, there are several related contaminant lists that are mostly aimed at crystallography. The original is ContaMiner (strube.cbrc.kaust.edu.sa/contaminer/c...) and there are lists underlying SIMBAD in CCP4 and, recently, phasertng.changeling (Phenix, soon CCP4). A list for cryoEM would be great!

ContaMiner

strube.cbrc.kaust.edu.sa

Josy ter Beek@josyterbeek.bsky.social · 3mo ago

Is there a good #contaminant checklist? Just had to tell a researcher that the sample they have been working on and I ran over the SEC-MALS for them, probably is the infamous ArnA his-tag purification contaminant from E. coli (100% Mw and ext. coeff. match). journals.iucr.org/d/issues/202...

Alisia Fadini@alisiafadini.bsky.social · 4mo ago

Access alternate functional conformations encoded in AlphaFold’s latent space in a few GPU minutes 👇 We also introduce a novel supervised transfer task: train once on a source (GPCR/kinase/transporter) and apply across the family. Work led by Minji!

Minji Lee@m1nj2.bsky.social · 4mo ago

We introduce ConforNets, a mechanism for conformational control in AlphaFold3 models - SoTA at producing diverse conformations on every multistate benchmark (N=104) - Novel capability: transfer state from one protein to another Outperforms BioEmu, ConforMix and AFsample3 🧵1/8

Melanie I Stefan@melanieistefan.bsky.social · 4mo ago

So, OpenAI, whose entire business model relies on some overhyped dudebros using vast amounts of stolen data and stolen labour, is releasing a specialised GPT for the life sciences. And naming it, apparently without any sense of irony or self-awareness. Rosalind.

John Rubinstein@johnrubinstein.bsky.social · 4mo ago

Sad news on the passing of Prof. Andreas Engel, a pioneer in the field of cryo-EM (shared with the 3DEM community by Henning Stahlberg). Andreas' kindness, warmth, and enthusiasm for science and his colleagues will be missed.

Dear colleagues, With deep sadness I share the news that Andreas Engel passed away last Wednesday, at the age of 82, after a courageous fight against an aggressive caner. Only half a year ago, he was out hiking in the Italian mountains with his wife Barbara, walking 160 km in a single week. Andreas trained as a physicist in Bern, Switzerland, before heading to John Hopkins University in Baltimore for his postdoctoral work. He then led a research group at the Biozentrum in Basel, and in 1985 took on the role of a group leader in research and development at Ilford Ltd. in Fribourg, Switzerland. In 1987, he joined forces with his colleague Ueli Aebi to establish the Maurice E. Müller Institute at the Biozentrum of the University of Basel. Together, Ueli and Andreas served as professors for structural biology there for almost a quarter century, leaving a lasting mark on the field of structural biology as we know it today. Andreas Engel was a true pioneer. He was among the first to apply atomic force microscopy (AFM) with the tip operating under water, and one of the earliest researchers to perform 3D reconstructions using scanning transmission electron microscopy, achieving remarkable high-resolution maps of porin 2D crystals by STEM. He became a leading expert in membrane protein 2D crystallization, and his group played a key role in the determination of the first aquaporin structure, in collaboration with Peter Agre and Yoshinori Fujiyoshi. As he approached retirement from Basel, Andreas founded the Center for Cellular Imaging and NanoAnalytics (C-CINA) of the University of Basel, which in 2009 operated among others one of the very early Titan Krios instruments. From 2008 also held a professorship at Case Western Reserve University, Cleveland, followed by a position at TU Delft in the Netherlands in 2013. In 2020, he was among the founding members of CryoWrite, a company in Basel that he led as CEO until recently. His contributions to science, to the tools of str…Photo of Andreas Engel
Hekstra Lab@hekstralab.bsky.social · 4mo ago

We're a big step closer to automated determination of protein structures. The key? Having AlphaFold listen to experimental data. Great work, led by @alisiafadini.bsky.social and @minhuanli.bsky.social in an inspiring collaboration with @moalquraishi.bsky.social and @randyjread.bsky.social.

Alisia Fadini@alisiafadini.bsky.social · 4mo ago

ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15

Minhuan Li@minhuanli.bsky.social · 4mo ago

ROCKET came out on Nature Methods today. It takes a tremendous amount of effort to translate a research concept into a practical tool—one that researchers can seamlessly drop into their existing pipelines. We learned a lot along the path and will carry that spirit forward.

Alisia Fadini@alisiafadini.bsky.social · 4mo ago

ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15

Mohammed AlQuraishi@moalquraishi.bsky.social · 4mo ago

Our heavily updated final version of ROCKET for experiment-guided structure modeling is out in @naturemethods! New frontiers like high-throughput fragment screening and mid-res tomography are forcing a rethink of how experiments are modeled. ROCKET+OpenFold proposes a solution👇

Alisia Fadini@alisiafadini.bsky.social · 4mo ago

ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15

Luca Jovine@jovinelab.org · 4mo ago

Very happy to have had a chance to attack an initially very low-resolution #cryo-EM map with #ROCKET! Thank you again @alisiafadini.bsky.social and all other co-authors of this important work, which truly shows the power of combining experimental structural biology and #AI inference. rdcu.be/fa9YH

Alisia Fadini@alisiafadini.bsky.social · 4mo ago

ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15

Minhuan Li@minhuanli.bsky.social · 5mo ago

It was a fantastic trip and a pleasure talking with the Pfizer team 😄 One highlight was discovering they’ve built a web GUI for ROCKET to make it more accessible—I’m thrilled (and even a bit surprised) to see how our tool helping people solve real-world problems.

Alisia Fadini@alisiafadini.bsky.social · 5mo ago

After an Amtrak coding session with @minhuanli.bsky.social, ROCKET team is back at @rs-station.bsky.social HQ! Thank you to Pfizer for welcoming us in Groton and to everyone who attended our seminar online. Exciting work ahead to continue exploring frontiers in structure determination. Back to it 🚀

Mohammed AlQuraishi@moalquraishi.bsky.social · 5mo ago

New OpenFold3 preview out! (OF3p2) It closes the gap to AlphaFold3 for most modalities. Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9

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