Calling all xray structure folks that have worked with denovo proteins. Do you suffer from high rfactors? Myself, someone else I know and now multiple structures all seem to suffer from this. Assuming we all tried our best in model building, what could be some causes?
The Critical Assessment of Structure Prediction (CASP) experiment is calling for prediction targets: Immune Complexes, Organic Ligand-Protein Complexes, Nucleic Acids and Complexes, Conformational Ensembles, Difficult Protein Structures and Complexes. Rule of Thumb: If AlphaFold3 can generate a high-quality model, it is likely not a CASP-grade challenge. If it struggles, we want it.
Is #AI hitting a plateau in structure prediction? Help us find out at CASP17! 🧪🧬
Calling for Targets: Immune Complexes, protein - ligand complexes, RNA/DNA, conformational ensembles, membrane proteins, viral origins, and large complexes.
The Rule of Thumb: If AF3 can’t model it, we want it.
2D classes of a 58 kDa particle collected on a 100 kev Tundra electron microscope
2D classes of the 58 kDa sample collected on the 100 keV Tundra TEM with a Falcon C detector at @nusbf.bsky.social @newcastleuni.bsky.social. Still much work to do to optimise the sample & data collection but its cool to see what a 100 keV TEM is capable of. #cryoEM @recon4imd.bsky.social
EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks pubmed.ncbi.nlm.nih.gov/41830330/ #cryoEM
6 women and 4 men pose on a staircase with floor-to-ceiling glass on the left side. A pop-up banner promoting the Scottish Centre for Macromolecular Imaging is in the foreground.
Last week, we hosted 6 participants on the Cryo-EM in Structural Biology 2026 course, part of our Wellcome/MRC-funded training programme. The course was hybrid with online lectures together with the other hosts and onsite practicals. Find out more: www.gla.ac.uk/research/az/...
I am incredibly excited to share that I will start my independent lab at the @unidue-zmb.bsky.social at the @unidue.bsky.social as Junior Professor of Cellular Biochemistry. Research in my lab has the goal to decipher the ubiquitin code!
There are multiple open positions!
(1/3)
CryoEM data collected at the ever helpful @scmicryoem.bsky.social
Comparison of PCNA and FANCD2
We call the SLiM found on these proteins a FANCD2-interacting protein box (DIP-box), as a shout-out to PCNA-interacting protein boxes (PIP-boxes)
Combining information from these structures with functional information from #uniprot and co-evolutionary information via #alphafold we found new FANCD2 interactors that utilize the same site
CryoEM consensus reconstructions of FANCI-FANCD2ub with FAN1 or CtIP
While figuring out the structural basis of FAN1 and CtIP interactions with the FANCD2 DNA clamp, we noticed a common interaction point that USP1 also uses
Excited to share our new paper uncovering how FANCD2 recognises various DNA repair proteins www.biorxiv.org/content/10.6... @hw1o9.bsky.social
We posted a biorxiv preprint on structural bioinformatics, AlphaFold modeling & machine learning on predicting specificity of E3 ligase ring domains for different E2 enzymes. 1/4
Preprint: www.biorxiv.org/content/10.6...
Models/data (UbiqCore website): dunbrack.fccc.edu/ubiqcore
AI in Protein Design: Hype vs. Reality Explained by David Baker
In this GEN interview, he emphasizes that designing new proteins from scratch is now a reality. Whether AI transforms medicine will require improving our understanding of biology's complexity
I love AlphaFold—but please include PAE (Predicted Aligned Error) plots for every “interaction.” Pretty PDBs ≠ proof. If the PAE doesn’t show an interface, it ain’t one. Show the plots. Structural biology's reputation is on the line.
Finally out in print! Long time project with @olexandr.bsky.social and the PHENIX group. Refinement of X-ray and CryoEM structures, using Machine Learned Potentials as the back end to help fitting. This fulfills the old dream of doing QM refinement, but very very cheap www.nature.com/articles/s41...
I wrote a blog post about the future of structural bioinformatics.
Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs?
Let me know what you think.
jgreener64.github.io/posts/struct...
Will Reform win the next UK election?
www.youtube.com/watch?v=mcu0...
RFdiffusion3 is here! We train a general network that explicitly models every atom and use it to design active enzymes and DNA binders.
Tremendous team effort with Jasper, Rohith, Raktim, Rafi, Yanjing, Paul, Jonathan, and many others!
Check it out: lnkd.in/eiUFfJaM.
This one is a bit of a departure from the usual and definitely a work in progress!
We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.
Read on for details... 1/x
Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...
You designed binders for your favourite protein and wish there was a way to experimentally screen them within 24h w/ only a set of pipettes and a plate reader?
Check out our Cell-Free 2-Hybrid approach (CF2H)
Full post: tinyurl.com/48cz5nb6
Preprint: www.biorxiv.org/cgi/content/...
I'm back. Here's how we fix the UK's dire economic and political situation www.youtube.com/watch?v=LMor...
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
This is quite something - 68% success rate for binder design w/ Chai 2, with many in the low-nM to pM range - impressive stuff chaiassets.com/chai-2/paper...
We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design!
github.com/martinpacesa...
The E3 ligase Parkin ubiquitinates many proteins. Koszela, Walden (@hw1o9.bsky.social) et al. @uofglasgow.bsky.social identify and biochemically validate a direct Parkin interaction with a substrate, Miro1. rupress.org/jcb/article/...
A nifty trick our lab is using to improve structure prediction of viral membrane proteins in #AlphaFold3! 👇
🧬 New from crystal structures from our lab in EMBO Journal! We reveal how the FANCM enzyme, an emerging therapeutic target it cancer, has evolved to specifically recognise branched DNA and activate the Fanconi anaemia pathway of DNA repair. doi.org/10.1038/s443... 🧵👇
I’m very happy to share my first paper on the effects of AWI interactions and flexibility on SPA data quality! Thank you to everyone on the team 🤩
www.sciencedirect.com/science/arti...
We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
