@jankosinski.bsky.social
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New method toward modeling cells and viruses! HMFF enables integrative membrane modeling and simulation guided by electron microscopy data. Created by Valentin Maurer and Marc Siggel
@embl.org
@cssbhamburg.bsky.social, in collaboration with @WPezeshkian lab (1/n)
www.biorxiv.org/content/10.1...
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6 months ago
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⏰ URGENT! ⏰ Into structural modeling, design, integration with experiments, evolution, or platforms? Join our conference, share your work, and see what’s hot! Only 4 days left to submit your abstract! 👇
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3 months ago
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EMBL Events
4 months ago
Join us at #EMBOComp3D to explore cutting-edge breakthroughs in computational structural biology, AI, drug design, and innovative software! 💻 Find out about molecular modelling to systems-level analyses and evolution, and more. Submit your abstract by 26 Aug ➡️
s.embl.org/csb25-01-bl
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One month remaining to register for our conference! Have a look at the outstanding speakers and programme, and use the link to join the 2nd edition of the Computational Structural Biology Conference in Heidelberg!
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4 months ago
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New method toward modeling cells and viruses! HMFF enables integrative membrane modeling and simulation guided by electron microscopy data. Created by Valentin Maurer and Marc Siggel
@embl.org
@cssbhamburg.bsky.social, in collaboration with @WPezeshkian lab (1/n)
www.biorxiv.org/content/10.1...
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6 months ago
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reposted by
Eva Kowalinski
7 months ago
Are you a postdoc ready for transition to an independent position? You connect infection biology with cutting-edge structural biology or multimodal imaging? Are you aware of such a colleague? I am seeking speakers for "The Next Generation in Infection Biology" microsymposium on June 6 2025.
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Centre for Structural Systems Biology CSSB
7 months ago
28 children spent the day at CSSB for Girls' and Boys' Day yesterday! The kids built microscopes, conducted chemistry and chromatography experiments, tried VR goggles and much more.
@carobarisch.bsky.social
@landaulabcssb.bsky.social
@jankosinski.bsky.social
@topf-lab.bsky.social
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We captured a snapshot of in-cell protein contact sites during influenza A virus infection. In-cell crosslinking, AlphaFold modeling, and functional follow-ups revealed new host factors and mechanisms. A step toward modeling the infected cell.
8 months ago
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Sorry Albert, I can't have coffee with you today because time is relative, and mine just ran out.
#chatgpt4o
8 months ago
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Draw a ribbon representation of a protein structure shaped like a banana, with alpha-helices, beta-sheets, and loops clearly visible, maintaining realistic molecular geometry and coloring styles typical for protein visualizations.
8 months ago
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reposted by
EMBL Events
9 months ago
Join us in Heidelberg for the 2nd edition of #EMBOComp3D! 🧬 Explore cutting-edge AI-driven innovations and classical methods in biomolecular research, new sessions on drug design, and make contacts during the job fair. Submit your abstract by 26 Aug 👉
s.embl.org/csb25-01-bl
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reposted by
EMBL Events
9 months ago
⏰ You have until 3 March to submit your abstract and be part of #EESInfection ➡️
https://s.embl.org/ees25-04-bl
🦠 🍄 This symposium will bring together researchers working on different pathogens and pave the way for new strategies to overcome current challenges in the treatment of infections 💡
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"We demonstrate that current co-folding approaches largely memorise ligand poses from their training data, hindering their use for de novo drug design."
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9 months ago
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Protein Data Bank in Europe (PDBe)
10 months ago
PDB-IHM (formerly PDB-Dev) is for integrative structures. Intergrative structures = from multiple experimental & computational methods. Since mid-2024 assigned PDB ids & DOIs. Access via wwPDB archive or PDB-IHM - pdb-ihm.org 👉
https://www.wwpdb.org/news/news?year=2025#677880ea44a8c95814022eb9
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reposted by
Ezgi Karaca
10 months ago
The legendary EMBO Integrative Modeling Course is back! If you want to be in this picture in the 2025 edition, just go ahead and register at
meetings.embo.org/event/25-bio...
Organized by myself &
@amjjbonvin.bsky.social
&
@arneelof.bsky.social
&
@lindorfflarsen.bsky.social
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reposted by
Peter Koo
11 months ago
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"Challenges along the way, but it worked out in the end"
youtu.be/HnT1VWzdFWc?...
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2024 Nobel Prize lectures in chemistry | David Baker, Demis Hassabis and John Jumper
YouTube video by Nobel Prize
https://youtu.be/HnT1VWzdFWc?t=4179
11 months ago
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Perhaps this is not the only time this picture will be shown during a Nobel Prize lecture 😉
11 months ago
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reposted by
Max Bonomi
11 months ago
Do you want to work at the interface of molecular simulations, structural biology experiments and
#AI
? Come to Paris for a PhD at
@pasteur.fr
1 PhD position is available in our lab funded by ERC_Research. Please repost!!
#compchem
#compbio
Info 👇
research.pasteur.fr/b/15Hr
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One PhD thesis in integrative structural biology | Research - Institut Pasteur
https://research.pasteur.fr/b/15Hr
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reposted by
Arne Elofsson
11 months ago
Conclusion for ligand session in
#casp16
, without a template methods fail
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Does anyone know of published test cases I can use to evaluate the approach? Ideally, the test case would feature a structure published after 30 September 2021, fail with AlphaFold3, and include real crosslinking data.
add a skeleton here at some point
11 months ago
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By the way, seeds are your friends when running AlphaFold 3. I use at least 20 by default.
11 months ago
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We have released version 2 of AlphaPulldown - a general pipeline for high-throughput structural modeling! Software:
github.com/KosinskiLab/...
Preprint:
biorxiv.org/content/10.1...
11 months ago
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Crosslinks can sometimes improve AlphaFold3 models. Crosslinking is an experimental method often used as a source of distance restraints in modeling. In AlphaFold3, instead of using restraints, crosslinks can be included as covalent ligands. Thanks to Agnieszka Obarska-Kosinska for the idea.
11 months ago
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reposted by
Arne Elofsson
12 months ago
Finally on board the Flight towards
#casp16
. If you want to see my talk you can find it here
m.youtube.com/watch?v=w1fG...
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CASP16 Lecture - Elofsson
YouTube video by Introduction to Bioinformatics by Arne Elofsson at Stockholm University
https://m.youtube.com/watch?v=w1fGdjM7iEU&t=10s
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#casp16
@arneelof.bsky.social
@amjjbonvin.bsky.social
what is the current state-of-the-art measure for reporting the quality of protein-protein docking models? sequence-dependent interface TM-score? Fnat? I guess not interface RMSD? What tool would you recommend to calculate all of them?
12 months ago
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reposted by
Konstantin Korotkov
12 months ago
Here is the plot for the protein complex predictions. AlphaFold3 server is an improvement over AlphaFold2 baseline represented by ColabFold.
#CASP16
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reposted by
Arne Elofsson
12 months ago
#CASP16
program is posted (so you can guess the "winners". Congratulations to Yang and Kihara who seems to have done well in RNA+Proteins. Also congratulations to AF3-server (i.e. me) who was selected to talk (i.e. most people did worse than the server).
predictioncenter.org/casp16/doc/C...
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https://predictioncenter.org/casp16/doc/CASP16_Meeting_Program.pdf
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reposted by
Arjen Jakobi
12 months ago
Really looking forward to welcoming & meeting the participants of our
#EMBOStructBio
course this morning! Many of our speakers/tutors are here:
@moalquraishi.bsky.social
@sykhalid.bsky.social
@ezgikaraca.bsky.social
@amjjbonvin.bsky.social
@gchojnowski.bsky.social
@drmelissagraewert.bsky.social
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reposted by
Andy Tseng
12 months ago
UPDATE:
Nature.com
has issued a correction: “Correction 14 November 2024: An earlier version of this article stated that AlphaFold3 is now ‘open source’. This is not the case, as weights for the model can only be accessed upon request, and the code can only be used for non-commercial applications.”
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AI protein-prediction tool AlphaFold3 is now more open
The code underlying the Nobel-prize-winning tool for modelling protein structures can now be downloaded by academics.
https://www.nature.com/articles/d41586-024-03708-4#correction-0
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Hello, I am Jan, and I like molecules and other molecules. Where is a bookmark post button?
12 months ago
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