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Joined September 2012
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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) doi.org/10.64898/2026.01.26.…
Chris LB Graham retweeted
Check out the latest from our lab. One of two papers published by @Behzaddeh who recently completed their PhD.
We identify CprV as a "safeguard" protein that protects cellular compartmentalisation during bacterial spore formation.
nature.com/articles/s42003-0…
Chris LB Graham retweeted
"we utilise coevolution to determine the likelihood of protein-protein interactions within proteins acting within the same biological pathway."
CoEVFold suite: user friendly pipelines to visually represent protein coevolution biorxiv.org/content/10.64898… #biorxiv_micrbio
Chris LB Graham retweeted
Check out these tools to detect co-evolution in protein-protein interactions developed by postdoc @ChrisLBGraham
Very useful as a hypothesis generator, complementing protein interaction prediction from Alphafold.
biorxiv.org/content/10.64898…
ConservFold was down, due to weblogo dependency issues... so ive replaced weblogo with ggseqlogo for now. Its back up again. thanks @omarwagih for the existence of your package.
colab.research.google.com/dr…
We have updated ConservFold. Now it can plot conservation onto whole protein complexes and you can set the cutoffs you’d like! Thought it might be useful for people! colab.research.google.com/dr… @CRodriguesLab
Chris LB Graham retweeted
Checkout out our computational framework, MemTorMD, for studying toroidal membranes of biological dimensions, present at division and fission sites. We studied lipid behaviour at these sites but also simulated membrane fission. Collaboration with @ChrisLBGraham and @pstansfeld
Just released a pre-print: biorxiv.org/content/10.1101/… We simulate lipid membrane toroids of bacteria, which represent the point just before one cell splits into two. We see they’re stable and then look at how a key protein might behave at them @pstansfeld @CRodriguesLab
Just released a pre-print: biorxiv.org/content/10.1101/… We simulate lipid membrane toroids of bacteria, which represent the point just before one cell splits into two. We see they’re stable and then look at how a key protein might behave at them @pstansfeld @CRodriguesLab
Chris LB Graham retweeted
🤯 Congratulations David Baker @UWproteindesign , @demishassabis and John Jumper!!
BREAKING NEWS
The Royal Swedish Academy of Sciences has decided to award the 2024 #NobelPrize in Chemistry with one half to David Baker “for computational protein design” and the other half jointly to Demis Hassabis and John M. Jumper “for protein structure prediction.”
Chris LB Graham retweeted
Exciting new work from Qian Cong's group on predicting human protein interactome. Leveraging new eukaryotic genomes, new RoseTTAFold2 trained on +/- pairs of PPI and large distilled dataset of domain-domain interactions! 🤩
biorxiv.org/content/10.1101/…
Chris LB Graham retweeted
The lowest cost of laboratory space in San Francisco starts at $1750/mo. What would happen if we dropped that cost by 10x? How many more ideas and experiments would take place?
Introducing Cellsius (cellsius.org/)
Chris LB Graham retweeted
🚨 job alert 🚨 Research technician role available working at University of Bristol with @ICadby !!! Ian is a fantastic scientist working on some very cool bacteria. Deadline is 11/06/2024 jobs.ac.uk/job/DHU247/resear…
Chris LB Graham retweeted
Dear Twitter sphere
Does anyone have a few mgs of durlobactam they could spare me please or know of a UK supplier? – at West Midlands, England
Chris LB Graham retweeted
Our work on the trajectories of scientists in the knowledge space has been published in EPJ Data Science @epj_ds! We show that tools for studying human mobility can be applied to the mobility within scientific knowledge.🧵
doi.org/10.1140/epjds/s13688…
Chris LB Graham retweeted
Check out the beautiful Cryo tomography of B. subtilis spores by Cecile Morlot @IBS and collaborators. A pleasure to have participated in this work.
nature.com/articles/s41467-0…
Chris LB Graham retweeted
Definitive proof that this sucrose selection system works.
Top Left: cells + plasmid on sucrose
Top Right: cells on sucrose
Bottom Left: cells + plasmid on glucose
Bottom Right: cells on glucose
Chris LB Graham retweeted
Something my friend Jeremy Tame @jeremytame1 wrote recently in Nature Chemistry about "Using symmetry to drive new protein assemblies"
nature.com/articles/s41557-0…
Chris LB Graham retweeted
A new version of AlphaPulldown by @dingquan_yu. Includes experimental support for multimeric templates in AlphaFold by @DmitryMolo90428 and interface to crosslink-based modeling AlphaLink2 of @RappsilberLab
github.com/KosinskiLab/Alpha…
We made a little conservation of amino acids tool, combining Weblogo and ColabFold, which you can run in the browser with a single sequence. Since some major conservation servers are down. Hope it's useful! rodrigueslab.com/resources @CRodriguesLab @pstansfeld @sokrypton
I cant understate how this is just attaching two existing tools together so thanks to the authors of weblogo, ColabFold and the MMSEQ2 server curators, but I've found it very useful myself so far.