Martin Rennie
@martinrennie.bsky.social
Biochemist/structural biologist who enjoys a bit of maths and programming
Pinned
Martin Rennie
@martinrennie.bsky.social
· Apr 22
Our review on #AlphaFold focussing on prediction classes beyond simple protein monomers (PPIs, conformational changes, protein-ligand complexes, etc) royalsocietypublishing.org/doi/10.1098/...
Reposted by Martin Rennie
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
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
AI in Protein Design: Hype vs. Reality Explained by David Baker
In this GEN interview, Nobel Laureate David Baker, PhD, emphasizes that designing proteins from scratch is reality and unpacks what's needed for AI to transform medicine.
www.genengnews.com
November 2, 2025 at 5:34 PM
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
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
Reposted by Martin Rennie
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.
October 24, 2025 at 5:44 PM
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.
Reposted by Martin Rennie
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...
AQuaRef: machine learning accelerated quantum refinement of protein structures - Nature Communications
AQuaRef employs machine learning to refine protein structures from cryo-EM and X-ray data in Phenix. It achieves quantum-level precision, improving model geometry and fit to the data while reducing ov...
www.nature.com
October 23, 2025 at 3:20 PM
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...
Reposted by Martin Rennie
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...
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...
Where next for structural bioinformatics?
jgreener64.github.io
October 15, 2025 at 2:16 PM
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...
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...
Reposted by Martin Rennie
Will Reform win the next UK election?
YouTube video by Garys Economics
www.youtube.com
September 21, 2025 at 8:38 AM
Reposted by Martin Rennie
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.
Tremendous team effort with Jasper, Rohith, Raktim, Rafi, Yanjing, Paul, Jonathan, and many others!
Check it out: lnkd.in/eiUFfJaM.
September 19, 2025 at 3:45 PM
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.
Tremendous team effort with Jasper, Rohith, Raktim, Rafi, Yanjing, Paul, Jonathan, and many others!
Check it out: lnkd.in/eiUFfJaM.
Reposted by Martin Rennie
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
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
September 13, 2025 at 12:05 AM
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
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
Reposted by Martin Rennie
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/...
and GH repo: github.com/refresh-bio/...
FAMSA2 enables accurate multiple sequence alignment at protein-universe scale
We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...
www.biorxiv.org
July 19, 2025 at 9:28 PM
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/...
and GH repo: github.com/refresh-bio/...
Reposted by Martin Rennie
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/...
Check out our Cell-Free 2-Hybrid approach (CF2H)
Full post: tinyurl.com/48cz5nb6
Preprint: www.biorxiv.org/cgi/content/...
July 17, 2025 at 11:42 AM
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/...
Check out our Cell-Free 2-Hybrid approach (CF2H)
Full post: tinyurl.com/48cz5nb6
Preprint: www.biorxiv.org/cgi/content/...
Reposted by Martin Rennie
I'm back. Here's how we fix the UK's dire economic and political situation www.youtube.com/watch?v=LMor...
I'm back – and I think we can win
YouTube video by Garys Economics
www.youtube.com
July 13, 2025 at 8:11 AM
I'm back. Here's how we fix the UK's dire economic and political situation www.youtube.com/watch?v=LMor...
Reposted by Martin Rennie
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
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
July 7, 2025 at 8:21 AM
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
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
Reposted by Martin Rennie
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...
July 2, 2025 at 3:19 PM
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...
Reposted by Martin Rennie
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...
github.com/martinpacesa...
June 30, 2025 at 7:45 PM
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...
github.com/martinpacesa...
Reposted by Martin Rennie
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/...
June 27, 2025 at 8:10 PM
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/...
Reposted by Martin Rennie
A nifty trick our lab is using to improve structure prediction of viral membrane proteins in #AlphaFold3! 👇
Amazingly, this gave us a high-confidence transmembrane channel for both mouse and human NS3, with oleic acids forming a bilayer-like pattern.
Our group now call this the “fatty acid hack.”
The #alphafold predictions with and without fatty acids shown below 👇
Our group now call this the “fatty acid hack.”
The #alphafold predictions with and without fatty acids shown below 👇
June 18, 2025 at 1:43 PM
A nifty trick our lab is using to improve structure prediction of viral membrane proteins in #AlphaFold3! 👇
Reposted by Martin Rennie
🧬 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... 🧵👇
June 2, 2025 at 12:42 AM
🧬 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... 🧵👇
Reposted by Martin Rennie
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...
www.sciencedirect.com/science/arti...
Untangling the effects of flexibility and the AWI in cryoEM sample preparation: A case study using KtrA
Single particle cryo-electron microscopy (cryoEM) is a powerful tool for elucidating the structures of biological macromolecules without requiring cry…
www.sciencedirect.com
June 2, 2025 at 5:18 PM
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...
www.sciencedirect.com/science/arti...
Reposted by Martin Rennie
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/
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/
May 22, 2025 at 10:10 AM
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/
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/
Reposted by Martin Rennie
New from #JRSocInterface: Emerging frontiers in protein structure prediction following the #AlphaFold revolution. Read more: royalsocietypublishing.org/doi/10.1098/...
April 21, 2025 at 4:13 PM
New from #JRSocInterface: Emerging frontiers in protein structure prediction following the #AlphaFold revolution. Read more: royalsocietypublishing.org/doi/10.1098/...
Our review on #AlphaFold focussing on prediction classes beyond simple protein monomers (PPIs, conformational changes, protein-ligand complexes, etc) royalsocietypublishing.org/doi/10.1098/...
April 22, 2025 at 4:46 PM
Our review on #AlphaFold focussing on prediction classes beyond simple protein monomers (PPIs, conformational changes, protein-ligand complexes, etc) royalsocietypublishing.org/doi/10.1098/...
Reposted by Martin Rennie
Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
April 8, 2025 at 12:17 PM
Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
@martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org
🧬 Code will be released in a couple weeks
Reposted by Martin Rennie
ChimeraX can run Foldseek to find similar structures, such as distantly related homologs, and analyze the results, for example, mapping all ligands onto your query structure. Here are ligands mapped onto Nipah virus G protein. www.rbvi.ucsf.edu/chimerax/dat...
March 6, 2025 at 11:06 PM
ChimeraX can run Foldseek to find similar structures, such as distantly related homologs, and analyze the results, for example, mapping all ligands onto your query structure. Here are ligands mapped onto Nipah virus G protein. www.rbvi.ucsf.edu/chimerax/dat...
Reposted by Martin Rennie
Briony Yorke @universityofleeds.bsky.social gave a talk at SoMB @uofglasgow.bsky.social about time resolved X-ray crystallography used to assess UV damage of crystallins (eye lens proteins-yours are as old as you are) #sketchnote #structuralbiology 🧪 bio-mat-sketches-mor.blogspot.com/2024/11/brio...
Briony Yorke: Seeing the light - the role of UV radiation in cataract formation
Sketch about the scientific talk by Briony Yorke about the detailed biochemistry on how crystalin proteins in the lens of the eye respond to UV.
bio-mat-sketches-mor.blogspot.com
November 27, 2024 at 6:02 PM
Briony Yorke @universityofleeds.bsky.social gave a talk at SoMB @uofglasgow.bsky.social about time resolved X-ray crystallography used to assess UV damage of crystallins (eye lens proteins-yours are as old as you are) #sketchnote #structuralbiology 🧪 bio-mat-sketches-mor.blogspot.com/2024/11/brio...
Reposted by Martin Rennie
Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1 pubmed.ncbi.nlm.nih.gov/39574680/
November 23, 2024 at 6:23 PM
Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1 pubmed.ncbi.nlm.nih.gov/39574680/
Reposted by Martin Rennie
Well, this is exciting. A 5 year postdoc position in my lab. Do ion channels appeal to you? What about calcium? This is going to be such a fun project!👇
my.corehr.com/pls/uogrecru...
my.corehr.com/pls/uogrecru...
'
my.corehr.com
November 16, 2024 at 9:08 PM
Well, this is exciting. A 5 year postdoc position in my lab. Do ion channels appeal to you? What about calcium? This is going to be such a fun project!👇
my.corehr.com/pls/uogrecru...
my.corehr.com/pls/uogrecru...