Chris LB Graham
@chrislbgraham.bsky.social
Research Fellow at University of Warwick.
Open Science, Proteins and Lipids.
Open Science, Proteins and Lipids.
Reposted by Chris LB Graham
Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure.
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
February 7, 2026 at 8:50 AM
Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure.
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)
Reposted by Chris LB Graham
🚨 New Research Alert!
Our team has discovered two new bacteriophages that target Serratia spp.—a major cause of hospital‑associated infections and a growing antibiotic‑resistance threat.
📄 Open‑access article in Journal of Applied Microbiology: doi.org/10.1093/jambio/lxag011
Our team has discovered two new bacteriophages that target Serratia spp.—a major cause of hospital‑associated infections and a growing antibiotic‑resistance threat.
📄 Open‑access article in Journal of Applied Microbiology: doi.org/10.1093/jambio/lxag011
Characterization of two novel bacteriophages infecting clinical isolates of Serratia spp. and therapeutic efficacy in a Galleria mellonella model of infection
AbstractAims. This study aimed to isolate virulent bacteriophages (phages) with the capacity to lyse clinical strains belonging to the genus Serratia. Furt
doi.org
February 2, 2026 at 10:01 PM
🚨 New Research Alert!
Our team has discovered two new bacteriophages that target Serratia spp.—a major cause of hospital‑associated infections and a growing antibiotic‑resistance threat.
📄 Open‑access article in Journal of Applied Microbiology: doi.org/10.1093/jambio/lxag011
Our team has discovered two new bacteriophages that target Serratia spp.—a major cause of hospital‑associated infections and a growing antibiotic‑resistance threat.
📄 Open‑access article in Journal of Applied Microbiology: doi.org/10.1093/jambio/lxag011
Reposted by Chris LB Graham
Excited to share our preprint that describes the mechanism of action of an historical infection remedy called Bald’s Eyesalve. In this preprint, we show that Bald’s Eyesalve has multifaceted mechanism of action against both S. aureus and A. baumannii (1/n).
February 3, 2026 at 10:25 AM
Excited to share our preprint that describes the mechanism of action of an historical infection remedy called Bald’s Eyesalve. In this preprint, we show that Bald’s Eyesalve has multifaceted mechanism of action against both S. aureus and A. baumannii (1/n).
Reposted by Chris LB Graham
iCASE PhD project available in my lab, combining microscopy method development with high throughput screening of bacteria. Applications to antibiotic drug discovery and screening for new cell division proteins. Collaboration with Cairn Research #microsky #bioimaging
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
Image-based bacterial phenotyping and antimicrobial drug discovery using smart high-throughput super-resolution microscopy at University of Warwick on FindAPhD.com
PhD Project - Image-based bacterial phenotyping and antimicrobial drug discovery using smart high-throughput super-resolution microscopy at University of Warwick, listed on FindAPhD.com
www.findaphd.com
February 2, 2026 at 11:11 AM
iCASE PhD project available in my lab, combining microscopy method development with high throughput screening of bacteria. Applications to antibiotic drug discovery and screening for new cell division proteins. Collaboration with Cairn Research #microsky #bioimaging
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
Reposted by Chris LB Graham
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
January 30, 2026 at 6:11 AM
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Reposted by Chris LB Graham
Check out these tools to detect co-evolution in protein-protein interactions developed by postdoc @chrislbgraham.bsky.social
Very useful as a hypothesis generator, complementing protein interaction prediction from Alphafold.
www.biorxiv.org/content/10.6...
Very useful as a hypothesis generator, complementing protein interaction prediction from Alphafold.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 27, 2026 at 8:55 AM
Check out these tools to detect co-evolution in protein-protein interactions developed by postdoc @chrislbgraham.bsky.social
Very useful as a hypothesis generator, complementing protein interaction prediction from Alphafold.
www.biorxiv.org/content/10.6...
Very useful as a hypothesis generator, complementing protein interaction prediction from Alphafold.
www.biorxiv.org/content/10.6...
We finally released a little coevolution pipeline, so you can add coevolution to predicted structures. With this you can understand more how proteins may genetically interact, as heteromers, homomers or hypothetical networks (or perhaps not) www.biorxiv.org/content/10.6...
January 27, 2026 at 8:16 AM
We finally released a little coevolution pipeline, so you can add coevolution to predicted structures. With this you can understand more how proteins may genetically interact, as heteromers, homomers or hypothetical networks (or perhaps not) www.biorxiv.org/content/10.6...
Reposted by Chris LB Graham
🌟 New Tool Alert!
We present MemPrO – a toolkit for orienting and building membrane protein systems:
✅ Membrane protein orientation ✅ Mixed membrane building ✅ Double membranes & curvature ✅ Peptidoglycan cell wall support
🔗 github.com/pstansfeld/mempro 📖 pubs.acs.org/doi/10.1021/...
We present MemPrO – a toolkit for orienting and building membrane protein systems:
✅ Membrane protein orientation ✅ Mixed membrane building ✅ Double membranes & curvature ✅ Peptidoglycan cell wall support
🔗 github.com/pstansfeld/mempro 📖 pubs.acs.org/doi/10.1021/...
MemPrO: A Predictive Tool for Membrane Protein Orientation
Membrane proteins play a vital role in numerous cellular processes, including ion transport, intercellular communication, and antibiotic resistance. Ensuring their accurate orientation within lipid bi...
pubs.acs.org
December 25, 2025 at 10:03 PM
🌟 New Tool Alert!
We present MemPrO – a toolkit for orienting and building membrane protein systems:
✅ Membrane protein orientation ✅ Mixed membrane building ✅ Double membranes & curvature ✅ Peptidoglycan cell wall support
🔗 github.com/pstansfeld/mempro 📖 pubs.acs.org/doi/10.1021/...
We present MemPrO – a toolkit for orienting and building membrane protein systems:
✅ Membrane protein orientation ✅ Mixed membrane building ✅ Double membranes & curvature ✅ Peptidoglycan cell wall support
🔗 github.com/pstansfeld/mempro 📖 pubs.acs.org/doi/10.1021/...
Reposted by Chris LB Graham
Fantastic to be part of this which was published today, Dr Nic Briggs and newly minted Dr Jack Stone from my lab did the experimental works that contributed to the paper with Christophe Grangeasse and colleagues. @warwicklifesci.bsky.social
And check out the accompanying paper from the Grangeasse lab: www.nature.com/articles/s41...
Streptococcus pneumoniae S protein activates PBP1a to regulate peptidoglycan remodelling and cell division - Nature Microbiology
S protein interacts with and activates PBP1a during cell division, as part of a larger GpsB-associated multiprotein complex that coordinates peptidoglycan remodelling in Streptococcus pneumoniae.
www.nature.com
December 19, 2025 at 11:43 AM
Fantastic to be part of this which was published today, Dr Nic Briggs and newly minted Dr Jack Stone from my lab did the experimental works that contributed to the paper with Christophe Grangeasse and colleagues. @warwicklifesci.bsky.social
Reposted by Chris LB Graham
Super collaboration with @raffaeleieva.bsky.social and @fronzeslab.bsky.social on the LptDEMY complex.
rdcu.be/eRxNf here our new study on the characterization of the lipopolysaccharide holotranslocon, LptDE and the newly identified subunits LptM and LptY. Great collaboration with @fronzeslab.bsky.social @pstansfeld.bsky.social @JulienMarcoux @YvesQuentin
Structural basis of lipopolysaccharide assembly by the outer membrane translocon holo-complex
Nature Communications - The asymmetric distribution of lipopolysaccharide (LPS) on the surface of the bacterial outer membrane is essential and crucial for antibiotic resistance. Here, authors...
rdcu.be
November 24, 2025 at 4:56 PM
Super collaboration with @raffaeleieva.bsky.social and @fronzeslab.bsky.social on the LptDEMY complex.
Reposted by Chris LB Graham
New paper alert! We used our fav technique, genetic suppression, to understand how FimX controls function of the T4P PilB motor ATPase in Pseudomonas aeruginosa. Great collab with the Ellison lab at U Georgia who helped with some fancy microscopy to capture pilus dynamics! doi.org/10.1371/jour...
Twitching motility suppressors reveal a role for FimX in type IV pilus extension dynamics
Author summary Type IV pili enable Pseudomonas aeruginosa to attach to surfaces, move (twitch), and form biofilms. Pilus extension is powered by the motor protein PilB, which is regulated by other fac...
doi.org
October 13, 2025 at 8:18 PM
New paper alert! We used our fav technique, genetic suppression, to understand how FimX controls function of the T4P PilB motor ATPase in Pseudomonas aeruginosa. Great collab with the Ellison lab at U Georgia who helped with some fancy microscopy to capture pilus dynamics! doi.org/10.1371/jour...
Reposted by Chris LB Graham
CaCoFold-R3D: a probabilistic model that predicts RNA 3D motifs and secondary structure using evolutionary information.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
All-at-once RNA folding with 3D motif prediction framed by evolutionary information - Nature Methods
CaCoFold-R3D is a probabilistic model that simultaneously predicts the RNA 3D motifs jointly with the secondary structure in a structural RNA using evolutionary information.
www.nature.com
October 3, 2025 at 1:25 PM
CaCoFold-R3D: a probabilistic model that predicts RNA 3D motifs and secondary structure using evolutionary information.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Chris LB Graham
GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio
www.nature.com/articles/s41...
www.nature.com/articles/s41...
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
September 18, 2025 at 8:09 PM
GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Chris LB Graham
Bit under the weather today, so stayed at home to write a paper…..instead I’ve made an image of a Lego bacterial outer membrane.
September 3, 2025 at 11:12 AM
Bit under the weather today, so stayed at home to write a paper…..instead I’ve made an image of a Lego bacterial outer membrane.
Reposted by Chris LB Graham
#microsky
We challenge the long-standing view that peptidoglycan alone protects cells from bursting.
Our study shows that the periplasm — enclosed by OM–PG connections — acts as a pressure buffer essential for osmoprotection in Gram-negative bacteria.
📄 www.nature.com/articles/s41...
We challenge the long-standing view that peptidoglycan alone protects cells from bursting.
Our study shows that the periplasm — enclosed by OM–PG connections — acts as a pressure buffer essential for osmoprotection in Gram-negative bacteria.
📄 www.nature.com/articles/s41...
Peptidoglycan–outer membrane attachment generates periplasmic pressure to prevent lysis in Gram-negative bacteria - Nature Microbiology
Outer membrane attachment to peptidoglycan enables periplasmic pressure to build up and counter cytoplasmic turgor pressure, preventing lysis during osmotic challenges in Escherichia coli.
www.nature.com
July 29, 2025 at 1:23 PM
#microsky
We challenge the long-standing view that peptidoglycan alone protects cells from bursting.
Our study shows that the periplasm — enclosed by OM–PG connections — acts as a pressure buffer essential for osmoprotection in Gram-negative bacteria.
📄 www.nature.com/articles/s41...
We challenge the long-standing view that peptidoglycan alone protects cells from bursting.
Our study shows that the periplasm — enclosed by OM–PG connections — acts as a pressure buffer essential for osmoprotection in Gram-negative bacteria.
📄 www.nature.com/articles/s41...
We have updated ConservFold. Now it can plot conservation onto whole protein complexes and can set the cutoffs you’d like! Thought it might be useful for people. colab.research.google.com/drive/1Lv-ak... @crodrigueslab.bsky.social
June 3, 2025 at 10:03 AM
We have updated ConservFold. Now it can plot conservation onto whole protein complexes and can set the cutoffs you’d like! Thought it might be useful for people. colab.research.google.com/drive/1Lv-ak... @crodrigueslab.bsky.social
Reposted by Chris LB Graham
Beta-lactams covalently bind to Penicillin Binding Proteins and have been the mainstay of antimicrobial chemotherapy for decades.
In this new paper with colleagues @Bicycle_tx we show a new way to hit old targets: rdcu.be/eoaRI
In this new paper with colleagues @Bicycle_tx we show a new way to hit old targets: rdcu.be/eoaRI
Discovery and chemical optimisation of a potent, Bi-cyclic antimicrobial inhibitor of Escherichia coli PBP3
Communications Biology - Discovery of a bicyclic peptide inhibitor of cell wall biosynthesis in the Enterobacterales demonstrates applicability of a modified phage display platform to antibiotic...
rdcu.be
May 28, 2025 at 10:30 AM
Beta-lactams covalently bind to Penicillin Binding Proteins and have been the mainstay of antimicrobial chemotherapy for decades.
In this new paper with colleagues @Bicycle_tx we show a new way to hit old targets: rdcu.be/eoaRI
In this new paper with colleagues @Bicycle_tx we show a new way to hit old targets: rdcu.be/eoaRI
Reposted by Chris LB Graham
"Revolutionary"? More like reclaiming wisdom!
👏 French farmers & scientists prove nature-based farming (no #pesticides, no synthetics), the way humans farmed for centuries, still delivers steady yields, stable incomes & boosts biodiversity after 30 years.
#ClimateAction
f24.my/BCO5.BS
👏 French farmers & scientists prove nature-based farming (no #pesticides, no synthetics), the way humans farmed for centuries, still delivers steady yields, stable incomes & boosts biodiversity after 30 years.
#ClimateAction
f24.my/BCO5.BS
Down to Earth - Chemical-free farming brings life back to rural France
Faced with widespread chemical pollution and a dramatic collapse in biodiversity, farmers and scientists in western France have been testing a revolutionary farming model for over 30 years. No pestici...
f24.my
May 27, 2025 at 8:03 AM
"Revolutionary"? More like reclaiming wisdom!
👏 French farmers & scientists prove nature-based farming (no #pesticides, no synthetics), the way humans farmed for centuries, still delivers steady yields, stable incomes & boosts biodiversity after 30 years.
#ClimateAction
f24.my/BCO5.BS
👏 French farmers & scientists prove nature-based farming (no #pesticides, no synthetics), the way humans farmed for centuries, still delivers steady yields, stable incomes & boosts biodiversity after 30 years.
#ClimateAction
f24.my/BCO5.BS
Reposted by Chris LB Graham
Another great collaboration where we studied the type IV SS of CPRs, which certainly opens new avenues for the study of these enigmatic (mostly epibiotic) organisms! @frvalera.bsky.social
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
The type IV secretion system of Patescibacteria is homologous to the bacterial monoderm conjugation machinery
The Candidate Phyla Radiation, also known as Patescibacteria, represents a vast and diverse division of bacteria that has come to light via culture-independent ‘omics’ technologies. Their limited bios...
www.microbiologyresearch.org
May 26, 2025 at 5:12 PM
Another great collaboration where we studied the type IV SS of CPRs, which certainly opens new avenues for the study of these enigmatic (mostly epibiotic) organisms! @frvalera.bsky.social
www.microbiologyresearch.org/content/jour...
www.microbiologyresearch.org/content/jour...
Reposted by Chris LB Graham
AlphaFold’s success builds on decades of tech advances, massive efforts to collect, curate, and share structural data, and rigorous benchmarking. What will it take to see a similar leap in structural ensemble prediction? @stephanieaw.bsky.social and I share some thoughts here 👇 Feedback is welcome!
Predicting macromolecular ensembles is incredibly promising. However, as no single experimental method can map a conformational ensemble’s full atomistic landscape, there are foundational questions: What exactly are we trying to predict, and how will we know when we have succeeded?
From Possibility to Precision in Macromolecular Ensemble Prediction
Proteins and other macromolecules do not exist in a single state but as dynamic ensembles of interconverting conformations, which are essential for functions such as catalysis, allosteric regulation, ...
arxiv.org
May 7, 2025 at 4:49 AM
AlphaFold’s success builds on decades of tech advances, massive efforts to collect, curate, and share structural data, and rigorous benchmarking. What will it take to see a similar leap in structural ensemble prediction? @stephanieaw.bsky.social and I share some thoughts here 👇 Feedback is welcome!
Reposted by Chris LB Graham
Just released a pre-print: www.biorxiv.org/content/10.1... We simulate lipid membrane toroids of bacteria, representing the point where one cell splits into two. We see they are stable and then look at how a key protein might behave at them @crodrigueslab.bsky.social @pstansfeld.bsky.social
May 3, 2025 at 7:00 AM
Just released a pre-print: www.biorxiv.org/content/10.1... We simulate lipid membrane toroids of bacteria, representing the point where one cell splits into two. We see they are stable and then look at how a key protein might behave at them @crodrigueslab.bsky.social @pstansfeld.bsky.social
Just released a pre-print: www.biorxiv.org/content/10.1... We simulate lipid membrane toroids of bacteria, representing the point where one cell splits into two. We see they are stable and then look at how a key protein might behave at them @crodrigueslab.bsky.social @pstansfeld.bsky.social
May 3, 2025 at 7:00 AM
Just released a pre-print: www.biorxiv.org/content/10.1... We simulate lipid membrane toroids of bacteria, representing the point where one cell splits into two. We see they are stable and then look at how a key protein might behave at them @crodrigueslab.bsky.social @pstansfeld.bsky.social
Reposted by Chris LB Graham
ChimeraX daily builds can predict small complexes of proteins, nucleic acids and small molecules using Boltz on your Mac, Windows or Linux computer without Nvidia graphics. www.rbvi.ucsf.edu/chimerax/dat...
May 1, 2025 at 12:35 AM
ChimeraX daily builds can predict small complexes of proteins, nucleic acids and small molecules using Boltz on your Mac, Windows or Linux computer without Nvidia graphics. www.rbvi.ucsf.edu/chimerax/dat...
Reposted by Chris LB Graham
Nature research paper: The distribution of subsurface microplastics in the ocean
https://go.nature.com/4iHBBKS
https://go.nature.com/4iHBBKS
The distribution of subsurface microplastics in the ocean - Nature
Global data collected between 2014 and 2024 provide insights into the distribution and potential transport mechanisms of subsurface microplastics throughout the oceanic water column.
go.nature.com
April 30, 2025 at 6:25 PM
Nature research paper: The distribution of subsurface microplastics in the ocean
https://go.nature.com/4iHBBKS
https://go.nature.com/4iHBBKS
Reposted by Chris LB Graham
A huge, new resource for plasmid research - PlasmidScope is a database of 852,000 #plasmid sequences with a rich set of annotations, automated online analysis and interactive visualisation academic.oup.com/nar/article/...
PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools
Abstract. Plasmids are extrachromosomal genetic molecules that replicate independent of chromosomes in bacteria, archaea, and eukaryotic organisms. They co
academic.oup.com
April 22, 2025 at 5:00 AM
A huge, new resource for plasmid research - PlasmidScope is a database of 852,000 #plasmid sequences with a rich set of annotations, automated online analysis and interactive visualisation academic.oup.com/nar/article/...