Elena Papaleo

MAVISp BioCurator Training 2025 Event Dates: 3rd to 5th of September 2025 (online) Check out details on the MAVISp website We can accommodate a maximum of 15 participants, on a first-come first-served basis If you have questions ...

We’re launching the 1st MAVISp BioCurator Training Workshop!
Learn to use MAVISp tools to assess structural impact of missense variants. Fully online | Free
Register by June 27, 2025:
docs.google.com/forms/d/e/1F...
See Events: services.healthtech.dtu.dk/services/MAV...
#bioinformatics #modeling

Point mutations of the mitochondrial chaperone TRAP1 affect its functions and pro-neoplastic activity Cell Death & Disease - Point mutations of the mitochondrial chaperone TRAP1 affect its functions and pro-neoplastic activity

Read our latest research with the Rasola Lab and @elenapapaleo.bsky.social on how mutations on the mitochondrial protein TRAP1 impact its function and cancer related activities, published with
@springernature on Cell Death and Disease in rdcu.be/edidL

PhD scholarship in AI Oracles for Fitness Landscape Optimization on Molecular Binders - DTU Health Tech As part of a joint research collaboration between DTU and Novo Nordisk, we are looking for a Ph.D.-candidate to join our multidisciplinary research program focusing on the interplay between AI-based p...

PhD Opportunity: AI-driven Protein Binder Design.
Join a cutting-edge DTU & Novo Nordisk collaboration! Work with AI, automation & protein engineering in a closed-loop design pipeline.
efzu.fa.em2.oraclecloud.com/hcmUI/Candid...
#PhD #AI #ProteinDesign #Bioinformatics #MachineLearning #Biology

Screenshot of Developer resources in Europe PMC. Use Europe PMC's Open Access content and metadata to build your applications. Articles RESTful API - Access publications and related information. Grants RESTful API - Access grant information from Europe PMC funders using the GRIST database. API case studies - Learn more about how Europe PMC APIs can be used to create new products and services. SOAP web service - Retrieve publication data using this Simple Object Access Protocol (SOAP)-based service. OAI service - Get access to the metadata of all items in the Europe PMC archive, and full text of a subset of these items. Bulk downloads - Download all the articles in the Open Access set, plus the metadata of all full-text articles in Europe PMC. Annotations API - Access annotations contained in abstracts and open access articles. Developer Forum - Join the developer forum to receive news about API releases, post general API questions, and share your experience with fellow API users. Tech Blog - Follow the Europe PMC Tech blog to learn about Europe PMC technical developments, API case studies and more.

Did you know Europe PMC offers powerful developer tools?

🔹 Articles API
🔹 Annotations API
🔹 Grants API
🔹 Bulk downloads
🔹 SOAP web service
🔹 OAI service And more!!

Find out more and access developer tools: europepmc.org/developers
#DeveloperTools #OpenSource #API #LiteratureSearch

The LC3-interacting region of NBR1 is a protein interaction hub enabling optimal flux, say Brian North, Christopher Shoemaker and colleagues: https://buff.ly/4b0ETa4

So grateful that our group contributed in this fantastic study on BRCA2 variants, congrats especially to Shyam Sharan and @sounaksahu.bsky.social - thank you for the opportunity of this journey together

Figure from the paper describing the alternating access model and text that says that relevant motions can be exceedingly subtle

A periodic reminder that biologically meaningful conformational changes do not have to be large

While textbooks may indicate that relevant motions are large, even the original paper on alternating access makes it clear that atoms just need to move a bit to have an effect. doi.org/10.1038/2119... 🧬🧶

A long-waited refinement tool for cofactors with metal-coordination, MetalCoord. By Garib Murshudov group @mrclmb.bsky.social
Compiles distances & angles from CCP4 monomer library and classifies the metal-coordination geometry. The updated dictionaries and restraints then used for refinement.

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.

www.biorxiv.org/content/10.1...

PLUMED Tutorials: a collaborative, community-driven learning ecosystem In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, ef...

📢 New #preprint describing our community effort to share #plumed tutorials arxiv.org/abs/2412.03595 ! Explore the tutorials at www.plumed-tutorials.org

Computational Care

DiffDock, a new diffusion-based ligand docking program, made s big splash earlier this year. But it’s apparently not all it’s claimed to be:

Doctoral Candidate positions within HORIZON – MSCA – 2023 – DN “STRIM: Scientific Training for Post-Translational Modification Detection in Cancer Screening” The STRIM Training Network “Scientific Training for Post-Translational Modification Detection in Cancer Screening” is a consortium of world leaders in bioinformatics and biomarkers discovery, biorecep...

PhD opportunities within a MSCA doctoral network STRIM
with my group.
DC11 Bioinformatics analysis to identify aberrant glycosylation and link them to clinical phenotypes
DC12 A bioinformatic integrative framework to study aberrant glycosylation euraxess.ec.europa.eu/jobs/290201

Stereochemistry in the disorder–order continuum of protein interactions - Nature Studies on protein–protein interactions using proteins containing d- or l-amino acids show that stereoselectivity of binding varies with the degree of disorder within the complex.

We did this crazy project where we tried to see if proteins could interact with their mirror image ligand. Seems impossible when proteins need to form 3D structures to interact. But what about if the interaction remains disordered???

www.nature.com/articles/s41...

Flyer for the course Keeping up with the interactome - How IDPs work including a list of speakers: Professor Tanja Mittag, St Jude Children’s Hospital, Memphis, US Professor Kresten Lindorff-Larsen, BIO, SCIENCE, UCPH Professor Ylva Ivarsson, Uppsala University, Sweden Dr. Michael Wehr, Systasy Bioscience, Munich, Germany Professor Zsuzsanna Dostztányi, Eötvös Loránd University, Hungary Professor Kristian Strømgaard, HEALTH, UCPH Professor Stefano Gianni, Sprienza University of Rome, Italy Professor Per Jemth, Uppsala University, Sweden Dr. Franziska Schöppe, Novo Nordisk A/S, Denmark Professor Benjamin Schuler, University of Zurich, Switzerland Professor Alfonse De Simone, University of Naples, Italy Dr. Malene Ringkjøbing Jensen, CNRS, Grenoble, France Alleyn Plowright, Chief Scientific Officer, Pangea Bio, London UK Professor Birthe B. Kragelund, BIO, SCIENCE, UCPH

If you are a PhD student and like protein disorder (or want to learn more), Birthe Kragelund @bbkrage.bsky.social and Kristian Strømgaard are organizing a PhD course on How IDPs work 🧶🧬🧪 Note the cost if you are not at a Danish university.

Details: phdcourses.ku.dk/DetailKursus...

Children who develop two independent tumors during childhood are extremely rare

We wanted to see if our genomic technologies could shed light into those exceptional cases.

Read about it in this recent paper:
tinyurl.com/yt9m584d

I would like to be added too 😊

Scholar Googler

Now online at JCTC:
“Is the Functional Response of a Receptor Determined by the Thermodynamics of Ligand Binding?”

Our answer: Yes, it is!
And we can use it to predict ligand efficacy.

pubs.acs.org/doi/10.1021/...

Interesting paper that explores the use of AlphaFold-Multimer in predicting Intrinsically disordered protein regions-protein complexes using in particular distogram data (minD) #alphafold #IDPs

paging @jessicaandreani.bsky.social @raphguerois.bsky.social

www.pnas.org/doi/10.1073/...

Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence Computational approaches can provide highly detailed insight into the molecular recognition processes that underlie drug binding, the assembly of prot…

Check out the issue of Curr Op Struct Biol on Protein Networks in Health and Disease! Advances in hybrid experimental-computational methods to study protein interactions & network-level function. #ComputationalBiology #ProteinNetworks

www.sciencedirect.com/science/arti...

Left, cry-EM structure of the complex between MIK2 (green), the immunoregulatory peptide SCOOP (yellow) and the LRR of the co-receptor BAK1 (white) with only the most rigid part of the N-glycans resolved (1 or 2 or none) and represented with sticks. Right, reconstruction of the N-glycosylation with plant N-glycans G90477LS,selected to be all the same as glycoproteomics data is not available (as far as I know)

If you are interested or working in #structuralbiology, as you see any protein (yes, *any*), you should be thinking: is it glycosylated? The answer is likely to be yes! You can predict N-glycosylation sites and rebuild all types of glycans with ReGlyco glycoshape.org 😌
Check out the example ⬇️ 1/2

Here are some free/open-source sites for the preparation of scientific illustrations, including icon libraries: bioicons.com, scidraw.io, bioart.niaid.nih.gov, inkscape.org, biogdp.com, reactome.org/icon-lib

Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!

Model does not run correctly on non A100/H100 GPUs · Issue #59 · google-deepmind/alphafold3 A note from us at Google DeepMind: We have now tested accuracy on V100 and there are serious issues with the output (looks like random noise). Users have reported similar issues with RTX 2060S and ...

We’ve now explored this on all GPU models available on our cluster and some non-A100/H100 do not have the issue; seems like something nuanced that can hopefully be fixed:
github.com/google-deepm...

AlphaFold can predict protein, DNA, or RNA complexes.. BUT is it easy to determine the reliable interactions?🤔

➡️ AlphaBridge will identify the most confident interactions, making your analysis easier!

🌐Try it here: alpha-bridge.eu
👀Read more: www.biorxiv.org/content/10.1...

Exploring structural diversity across the protein universe with The Encyclopedia of Domains The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted protein structures composed of domains, which are independently folding units found in multiple structural and ...

Hi TED! 👋
Out now in Science, we are finally ready to make our classification of all domains in AFDB v4 available to all!
A joint effort of @cathgene3d.bsky.social and the Jones group (PSIPRED), here's a link to the article

www.science.org/doi/10.1126/...

1/6 🧵⤵️

4 days of great science in a cozy venue for the #CECAM workshop www.cecam.org/workshop-det... in Paris

Jurgen in our group run AF3 locally after fiddling. It worked well on a A100 and produced some bad models on a lower end GPU. We don't have access to many A100s so unless we get it working on lower-end GPUs we won't be able to use this much.

Teresa Carlomagno standing in front of the room

3rd day of our #CECAM workshop on biomolecular interfaces dynamics, Teresa opens the morning session on IA and integrative approaches.

eLife won’t get an impact factor, says Clarivate Clarivate, the data company for scholarly publications, has decided to continue indexing some content from eLife in Web of Science, after reevaluating the open-access biology journal’s unusual prac…

#eLife will not have a IF score, says Clarivate ➡️ retractionwatch.com/2024/11/13/e...

This will be the ultimate test of how much we care about an absurd metric vs the *actual* quality of the journal I personally love eLife, had a fantastic experience both as an author and as a reviewer 🔝⭐⭐⭐⭐⭐