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Reposted by Katja Luck

protaiomics.bsky.social @protaiomics.bsky.social · 5d

🌟Ready to apply?
16 fully funded PhD positions are open in ProtAIomics Doctoral Network!
Join 16 labs across Europe to advance AI-powered proteomics and drive discoveries in health & biotechnology.
👉 Apply here: www.protaiomics.eu
#Proteomics #ArtificialIntelligence #MSCA #PhDOpportunities

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Reposted by Katja Luck

protaiomics.bsky.social @protaiomics.bsky.social · 3d

Researchers from any country🌍can apply to ProtAIomics->
No PhD yet
Mobility rule applies (≤12 months in host country in last 3 years)
Must meet host/project requirements
Details 👉 www.protaiomics.eu/call-for-app...

#Proteomics #ArtificialIntelligence #MSCA #PhDOpportunities #FullyFundedPhD

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Reposted by Katja Luck

Ylva Ivarsson @ivarssonlab.bsky.social · 21d

Finally out! Thrilled to share our collaboration with @kulathu.bsky.social, @orafurman.bsky.social, and N Davey. We screened auxiliary domains of USP family #deubiquitinases, revealing short linear motifs (SLiMs), contributing to specificity in complex assembly.
www.biorxiv.org/content/10.1...

Systematic Discovery of Motif-based Interactions of the Auxiliary Domains of USP Family Deubiquitinases

The ubiquitin-specific proteases (USPs) family is the largest family of human deubiquitinating enzymes (DUBs). While most USPs are agnostic to polyubiquitin linkage-type, their substrate specificity i...

www.biorxiv.org

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Reposted by Katja Luck

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 6d

The proteasome-substrate-shuttle protein UBQLN2 contains—like other quality control system proteins—a long region devoid of lysine (a lysine desert)

Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation

doi.org/10.1101/2025...

Fig. 1 – UBQLN2 is a conserved lysine-depleted protein. (A) Sequence comparison of
UBQLN2 orthologs in the indicated species. Intrinsically disordered regions in human
UBQLN2 based on MobiDB are shown as a blue bar. The domain organization based on the
SMART database is marked. Lysine residues are marked as black squares. (B) ESM-2
predictions of all possible single amino acid substitutions of human UBQLN2 presented as a
heat map. The wild-type residues are marked in blue. ESM-2 scores close to zero (light
yellow colors) indicate that the amino acid substitution is compatible with the ESM-2
language model, whereas negative scores (dark orange colors) indicate that the variant is
incompatible with the ESM-2 model. The domain organization (based on SMART) is aligned
above the map. Note that substitutions to lysine or cysteine in general appear detrimental, in
particular downstream of the UBL domain. (C) The AlphaFold2 predicted structured of
human UBQLN2 (AF-Q9UHD9-F1) (left panel). The UBL domain is colored blue, and the
UBA domain is colored orange and the STI1 regions green. Zoom in on the UBL domain
(right panel) with the lysine residues highlighted as stick representations and colored based
on the relative accessible surface area (rASA, dark red exposed; grey, buried).

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Reposted by Katja Luck

Pedro Beltrao @pedrobeltrao.bsky.social · 4d

new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...

The functional landscape of the human ubiquitinome

Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...

www.biorxiv.org

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Reposted by Katja Luck

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 27d

pip install ipsae
from www.linkedin.com/in/ullah-sam...

www.youtube.com/watch?v=A5ph...
PyPI pypi.org/project/ipsae/
His github fork github.com/ullahsamee/I...
My github github.com/DunbrackLab/...
Paper www.biorxiv.org/content/10.1...
For designed protein binders www.biorxiv.org/content/10.1...

Screen binders using ipSAE

YouTube video by ProteinDesignStudio

www.youtube.com

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Reposted by Katja Luck

Institute of Molecular Biology (IMB) @imbmainz.bsky.social · Sep 10

Our IPP Winter Call is now open! 📢 Are you looking for a fully funded PhD project in an international environment, doing cutting-edge research, and developing your career with advanced training? Join the #IPPMainz!

Learn more via www.imb.de/phd & apply by 16 October

#IMBMainz @unimainz.bsky.social

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Katja Luck @katjaluck.bsky.social · Sep 10

Open PhD position in the Luck lab at IMB in Mainz, Germany, in the field of AI and computational structural biology. Check out project description here: www.imb.de/students-pos...
Funded as part of the European Training Network ProAIomics cordis.europa.eu/project/id/1...

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Reposted by Katja Luck

jackie pelham @pelhamjackie.bsky.social · Aug 27

New IDPSeminars season on deck 🤩

We hope you can join us to learn about some exciting science!

More info in the post below👇

IDPSeminars @idpseminars.bsky.social · Aug 27

🚨🚨IDPSeminars is BACK 🚨🚨

Season 19 (!) gets underway next week with @rohitpappu68.bsky.social and Meredith Jackrel!

Date: Thur. Sept 4th
Time: 1 pm EST [USA] / 7 pm CET [Europe]

If you've previously signed up, you should be good to go, otherwise, please sign up at idpseminars.com

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Reposted by Katja Luck

Ben Lehner @benlehner.bsky.social · Jun 25

New preprint: Allostery is a widespread cause of loss-of-function variant pathogenicity by the great
@xt117.bsky.social
biorxiv.org/content/10.1...

Allostery is a widespread cause of loss-of-function variant pathogenicity

Allosteric communication between non-contacting sites in proteins plays a fundamental role in biological regulation and drug action. While allosteric gain-of-function variants are known drivers of onc...

biorxiv.org

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Reposted by Katja Luck

Norwegian Centre for Molecular Biosciences and Medicine (NCMBM) @ncmbm.bsky.social · Jun 30

📣 We’re recruiting 1-2 Group Leaders! NCMBM is looking for early-career researchers ready to establish their independent research groups!

🧬 With an attractive start-up package, help us shape the future of molecular biosciences and medicine in 🇳🇴 and be part of the @nordicembl.bsky.social!

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Katja Luck @katjaluck.bsky.social · Jul 1

Variant characterization in the intrinsically disordered human proteome - here is how we did it using short linear motif prediction, AlphaFold, and experimentation. Check out our preprint: www.biorxiv.org/cgi/content/...

Variant characterization in the intrinsically disordered human proteome

Variant effect prediction remains a key challenge to resolve in precision medicine. Sophisticated computational models that exploit sequence conservation and structure are increasingly successful in t...

www.biorxiv.org

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Reposted by Katja Luck

SFB 1551 - Collaborative Research Centre 1551 @sfb1551.bsky.social · May 22

🚨Publication alert🚨
"Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates" by Emanuele Zippo, @lstelzl.bsky.social, @dormannlab.bsky.social & Thomas Speck. Congratulations!!
📄 www.nature.com/articles/s41...
#TDP43 #CK1δ #ALS #biophysics #proteincondensates

Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates - Nature Communications

Here, the authors implement molecular dynamics simulations to model ATP-driven enzymatic reactions, revealing how the enzyme CK1δ phosphorylates condensates of the neurodegeneration linked protein TDP...

www.nature.com

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Reposted by Katja Luck

biomolstructure.bsky.social @biomolstructure.bsky.social · Mar 24

meetings.embo.org/event/25-str...
#EMBOStructuralBio

When predictions meet experiments: the next challenges in structural biology

Building on the success of the 2022 EMBO Workshop “When Predictions Meet Experiments: The Future of Structure Determination”, this second edition continues the journey at the interface of computation…

meetings.embo.org

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Reposted by Katja Luck

ME Torres-Padilla @metorrespadilla.bsky.social · Jun 12

Are you @ the late stages of your postdoc ? Want to pursue a PI career ?

Then this 👇👇 is for you ! Apply for a spot @ our Talent Forum
www.helmholtz-munich.de/en/stem-cell...

Peer-networking / Career orientation and more !!!

Please distribute :) 🙂

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Reposted by Katja Luck

Pedro Beltrao @pedrobeltrao.bsky.social · Jun 9

New lab preprint - Delora Baptista tested AlphaFold 2 and 3 for the prediction of structures of host-pathogen interactions and then applied these to study convergence of binding and molecular mimicry in host-pathogen vs. host-host interactions.
www.biorxiv.org/content/10.1...

AlphaFold models of host-pathogen interactions elucidate the prevalence and structural modes of molecular mimicry

Pathogens exploit host cellular machinery through protein-protein interactions (PPIs), often using molecular mimicry to hijack host cellular processes. While there have been thousands of host-pathogen...

www.biorxiv.org

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Reposted by Katja Luck

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · May 15

We've updated our AFESM website to now include biome filtering, allowing exploration of protein structures adapted to specific environments.
🌐 afesm.foldseek.com
Read more about the work in the skeetorial
🦋 bsky.app/profile/mart...
or our preprint
📄 www.biorxiv.org/content/10.1...

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Reposted by Katja Luck

SPP2191 - Molecular Mechanisms of Functional Phase Separation @spp2191.bsky.social · May 16

📢 Registration is open for the GBM Compact: Focus on Condensate Biology & SPP2191 Satellite Meeting! This is sure to be an incredible event diving into the latest in phase separation research with leading scientists.
📍 Frankfurt am Main
📅 Sept 16–19, 2025
🌐 shorturl.at/ZGQch
@gbmev.bsky.social

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Reposted by Katja Luck

Evangelia Petsalaki @epetsalaki.bsky.social · May 16

We present SELPHI 2.0 a machine learning model integrating >40 sequence, omics and structural features to predict kinase-substrate interactions between 420 kinases and 240K phosphosites and improve interpretation of global phosphoproteomics data www.sciencedirect.com/science/arti...

Data-driven extraction of human kinase-substrate relationships from omics datasets

Phosphorylation forms an important part of the signalling system that cells use for decision making and regulation of processes such as cell division …

www.sciencedirect.com

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Reposted by Katja Luck

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · May 15

Led by @vvouts.bsky.social in @rhp-lab.bsky.social, we measured the degron potency of >200,000 30-residue tiles from >5,000 cytosolic human proteins and trained an ML model for degrons

📜 www.biorxiv.org/content/10.1...
🖥️ github.com/KULL-Centre/...

Rasmus Hartmann-Petersen @rhp-lab.bsky.social · May 15

In collaboration with the @lindorfflarsen.bsky.social group we release our map of degrons in >5,000 human cytosolic proteins with >99% coverage. A machine learning model trained on the data identifies missense variants forming degrons in exposed & disordered regions. Work led by @vvouts.bsky.social.

A complete map of human cytosolic degrons and their relevance for disease

Degrons are short protein segments that target proteins for degradation via the ubiquitin-proteasome system and thus ensure timely removal of signaling proteins and clearance of misfolded proteins fro...

www.biorxiv.org

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Reposted by Katja Luck

Michael Bronstein @mmbronstein.bsky.social · May 3

Join us in Vienna on Sep 8-10 with an incredible speaker lineup!

AITHYRA Research Institute of the Austrian Academy of Sciences @aithyra.bsky.social · May 2

Please save-the-date for the #AITHYRA Symposium “AI for Life Science”, which will take place in Vienna at the House of Industry from 8-10 September 2025. Great speakers, interesting framework programme and beautiful location. Registration will open mid May. More info: www.oeaw.ac.at/aithyra/news...

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Reposted by Katja Luck

Arne Elofsson @bioinfo.se · May 5

In this evaluation of AlphaFold3 (and other methods), we show that (i) accurate predictions are limited to RNA structures/complexes with structural similarity to PDB and (ii) that current methods are bad at estimating the accuracy of the predictions. www.biorxiv.org/content/10.1...

Limits of deep-learning-based RNA prediction methods

Motivation: In recent years, tremendous advances have been made in predicting protein structures and protein-protein interactions. However, progress in predicting the structure of RNA, either alone or...

www.biorxiv.org

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Reposted by Katja Luck

Sergio Cruz-León @sergiocruzleon.bsky.social · Apr 11

Excited to share our preprint on the molecular architecture of heterochromatin in human cells 🧬🔬w/ @jpkreysing.bsky.social, @johannesbetz.bsky.social,
@marinalusic.bsky.social, Turoňová lab, @hummerlab.bsky.social @becklab.bsky.social @mpibp.bsky.social

🔗 Preprint here tinyurl.com/3a74uanv

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Reposted by Katja Luck

Gräter lab @graeterlab.bsky.social · Apr 4

Job alert: Join us in Mainz as

Max Planck Research Group Leader (W2) in Molecular Design

...and make your own research dreams happen on de novo design, generative models, proteins, materials ...
tinyurl.com/r2xjxnuk

@mpip-mainz.mpg.de

Max Planck Research Group Leader (W2) in Molecular Design

We are looking for exceptional early-career scientists conducting computational research with a proven record of accomplishment. The primary focus of this call is on candidates proposing research on b...

tinyurl.com

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