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Reposted by Chris LB Graham

Nature Methods @natmethods.nature.com · 5d

CaCoFold-R3D: a probabilistic model that predicts RNA 3D motifs and secondary structure using evolutionary information.

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

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Reposted by Chris LB Graham

Nature Methods @natmethods.nature.com · 20d

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...

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

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Reposted by Chris LB Graham

Syma Khalid @sykhalid.bsky.social · Sep 3

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.

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Reposted by Chris LB Graham

Michael Deghelt @michaeldeghelt.bsky.social · Jul 29

#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...

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

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Chris LB Graham @chrislbgraham.bsky.social · Jun 3

@crodrigueslab.bsky.social

Chris LB Graham @chrislbgraham.bsky.social · Jun 3

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

davidroper2.bsky.social @davidroper2.bsky.social · May 28

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

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

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Reposted by Chris LB Graham

Slow Food @slowfoodhq.bsky.social · May 27

"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

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

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Reposted by Chris LB Graham

Pedro J. Cabello-Yeves @pedrojcy91.bsky.social · May 26

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...

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

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Reposted by Chris LB Graham

Max Bonomi @bonomimax.bsky.social · May 7

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!

Stephanie Wankowicz @stephanieaw.bsky.social · May 6

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

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Reposted by Chris LB Graham

Chris LB Graham @chrislbgraham.bsky.social · May 3

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

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Chris LB Graham @chrislbgraham.bsky.social · May 3

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

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Chris LB Graham @chrislbgraham.bsky.social · May 2

Have you got a website with quotes to share?

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Reposted by Chris LB Graham

ChimeraX @chimerax.ucsf.edu · May 1

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...

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Reposted by Chris LB Graham

Nature @nature.com · Apr 30

Nature research paper: The distribution of subsurface microplastics in the ocean

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

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Chris LB Graham @chrislbgraham.bsky.social · Apr 26

a group of people are dancing in a forest with the words `` hoppity hobbity '' written on the bottom of the image .

ALT: a group of people are dancing in a forest with the words `` hoppity hobbity '' written on the bottom of the image .

media.tenor.com

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Reposted by Chris LB Graham

Taylor priest @taylorpriest.bsky.social · Apr 22

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

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Reposted by Chris LB Graham

eLife @elife.bsky.social · Apr 14

Introducing SAVEMONEY, AKA ‘Simple Algorithm for Very Efficient Multiplexing of Oxford Nanopore Experiments for You’

A new tool offering a faster, cheaper computational approach to democratise whole-plasmid sequencing.
buff.ly/ov7YumB

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Reposted by Chris LB Graham

Raffaele Ieva @raffaeleieva.bsky.social · Apr 11

Here our new preprint on the LPS holo-translocon doi.org/10.1101/2025... , collaboration with Yves Quentin @JulieMarcoux @fronzeslab.bsky.social @pstansfeld.bsky.social - @cbitoulouse.bsky.social

Structural Basis of Lipopolysaccharide Assembly by the Outer Membrane Translocon Holo-Complex

Lipopolysaccharide (LPS) assembly at the surfaces-exposed leaflet of the bacterial outer membrane (OM) is mediated by the OM LPS translocon. An essential transmembrane beta-barrel protein, LptD, and a...

doi.org

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Chris LB Graham @chrislbgraham.bsky.social · Apr 11

Bit crazy but could you restrict the ends off it? Hope you find a solution

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Chris LB Graham @chrislbgraham.bsky.social · Apr 11

Try genscript they will print this. I go to them in times of need.

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Chris LB Graham @chrislbgraham.bsky.social · Apr 8

(Or wolves)

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Chris LB Graham @chrislbgraham.bsky.social · Apr 8

I agree with your statement.. it’s showing the fallacy

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Chris LB Graham @chrislbgraham.bsky.social · Apr 8

I find de extinction of mammoths to at least to have some basis in a human caused event being rectified and useful in tundra grasslands where we no longer have megafauna. But dire wolves, are they meant to be reintroduced as a predator? we have tigers in the areas mammoths might be considered

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Reposted by Chris LB Graham

Allister Crow @allistercrow.bsky.social · Apr 7

New preprint!

FtsEX-EnvC is a Type VII ABC transporter that activates the periplasmic enzymes needed to break the peptidoglycan layer during cell division.

We tested the importance of structural features underpinning activation and the auto-inhibition mechanism that keeps it all in check.

Probing the mechanism of peptidoglycan amidase activation by FtsEX-EnvC

The FtsEX-EnvC-AmiA/B system is a key component of the E. coli cell division machinery that directs breakage of the peptidoglycan layer during separation of daughter cells. Structural and mechanistic ...

www.biorxiv.org

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