@jankosinski.bsky.social
Pinned
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...
⏰ 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! 👇
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
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
August 22, 2025 at 11:53 AM
⏰ 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! 👇
Reposted
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
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
July 24, 2025 at 11:14 AM
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
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
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!
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!
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
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
July 28, 2025 at 4:53 PM
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!
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!
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...
May 30, 2025 at 8:36 PM
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...
Reposted
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.
I am seeking speakers for "The Next Generation in Infection Biology" microsymposium on June 6 2025.
April 16, 2025 at 8:16 AM
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.
I am seeking speakers for "The Next Generation in Infection Biology" microsymposium on June 6 2025.
Reposted
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
@carobarisch.bsky.social @landaulabcssb.bsky.social @jankosinski.bsky.social @topf-lab.bsky.social
April 4, 2025 at 11:40 AM
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
@carobarisch.bsky.social @landaulabcssb.bsky.social @jankosinski.bsky.social @topf-lab.bsky.social
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.
March 29, 2025 at 1:55 PM
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.
Sorry Albert, I can't have coffee with you today because time is relative, and mine just ran out. #chatgpt4o
March 28, 2025 at 3:15 PM
Sorry Albert, I can't have coffee with you today because time is relative, and mine just ran out. #chatgpt4o
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.
March 27, 2025 at 8:15 AM
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.
Reposted
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
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
February 24, 2025 at 12:49 PM
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
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
Reposted
⏰ 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 💡
🦠 🍄 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 💡
February 6, 2025 at 1:04 PM
⏰ 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 💡
🦠 🍄 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 💡
"We demonstrate that current co-folding approaches largely memorise ligand poses from their training data, hindering their use for de novo drug design."
Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Have protein-ligand co-folding methods moved beyond memorisation?
Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...
www.biorxiv.org
February 9, 2025 at 3:37 PM
"We demonstrate that current co-folding approaches largely memorise ligand poses from their training data, hindering their use for de novo drug design."
Reposted
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
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
January 17, 2025 at 1:35 PM
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
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
Reposted
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
Organized by myself & @amjjbonvin.bsky.social & @arneelof.bsky.social & @lindorfflarsen.bsky.social
January 2, 2025 at 8:57 AM
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
Organized by myself & @amjjbonvin.bsky.social & @arneelof.bsky.social & @lindorfflarsen.bsky.social
Reposted
"Challenges along the way, but it worked out in the end" youtu.be/HnT1VWzdFWc?...
2024 Nobel Prize lectures in chemistry | David Baker, Demis Hassabis and John Jumper
YouTube video by Nobel Prize
youtu.be
December 8, 2024 at 4:25 PM
"Challenges along the way, but it worked out in the end" youtu.be/HnT1VWzdFWc?...
Perhaps this is not the only time this picture will be shown during a Nobel Prize lecture 😉
December 8, 2024 at 4:16 PM
Perhaps this is not the only time this picture will be shown during a Nobel Prize lecture 😉
Reposted
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
One PhD thesis in integrative structural biology | Research - Institut Pasteur
research.pasteur.fr
December 6, 2024 at 8:31 AM
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
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.
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.
December 4, 2024 at 7:16 PM
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.
By the way, seeds are your friends when running AlphaFold 3. I use at least 20 by default.
December 4, 2024 at 3:23 PM
By the way, seeds are your friends when running AlphaFold 3. I use at least 20 by default.
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...
Software: github.com/KosinskiLab/...
Preprint: biorxiv.org/content/10.1...
December 4, 2024 at 10:02 AM
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...
Software: github.com/KosinskiLab/...
Preprint: biorxiv.org/content/10.1...
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.
December 4, 2024 at 9:40 AM
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.
Reposted
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...
CASP16 Lecture - Elofsson
YouTube video by Introduction to Bioinformatics by Arne Elofsson at Stockholm University
m.youtube.com
December 2, 2024 at 1:49 PM
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...
#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?
December 2, 2024 at 3:56 PM
#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?