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/...
paging @jessicaandreani.bsky.social @raphguerois.bsky.social
www.pnas.org/doi/10.1073/...
November 20, 2024 at 7:22 AM
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/...
paging @jessicaandreani.bsky.social @raphguerois.bsky.social
www.pnas.org/doi/10.1073/...
AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface
www.nature.com/articles/s41...
#plantscience
www.nature.com/articles/s41...
#plantscience
AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface - Nature Comm...
AlphaFold-Multimer was used to screen of 1,879 small secreted proteins from plant pathogens to be inhibitors of six tomato defense enzymes. Four of these inhibit subtilase P69B, showing the use of AI ...
www.nature.com
September 27, 2023 at 8:30 PM
AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface
www.nature.com/articles/s41...
#plantscience
www.nature.com/articles/s41...
#plantscience
Very excited to share that my thesis work is out in Molecular Cell! We trained a Structure and Omics informed Classifier (SPOC) to score binary AlphaFold multimer (AF-M) predictions by structural quality and consistency with experimental omics datasets. www.cell.com/molecular-ce...
Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions
Schmid and Walter train a classifier that discerns functionally relevant structure
predictions in proteome-wide protein-protein interaction (PPI) screens using AlphaFold-Multimer,
and they use this co...
www.cell.com
February 26, 2025 at 6:14 PM
Very excited to share that my thesis work is out in Molecular Cell! We trained a Structure and Omics informed Classifier (SPOC) to score binary AlphaFold multimer (AF-M) predictions by structural quality and consistency with experimental omics datasets. www.cell.com/molecular-ce...
"AlphaFold-Multimer’s prediction accuracy is sensitive to the defined boundaries of the interacting partners" #alphafold
yep
www.pnas.org/doi/10.1073/...
yep
www.pnas.org/doi/10.1073/...
AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions | PNAS
Interactions mediated by intrinsically disordered protein regions (IDRs) pose formidable
challenges in structural characterization. IDRs are highly...
www.pnas.org
September 30, 2025 at 7:57 AM
"AlphaFold-Multimer’s prediction accuracy is sensitive to the defined boundaries of the interacting partners" #alphafold
yep
www.pnas.org/doi/10.1073/...
yep
www.pnas.org/doi/10.1073/...
New video 🎥
The AlphaFold-Multimer prediction for your protein looks great. But how confident should you actually be in it?
Razan Abbara breaks down the 5 confidence metrics behind every AFDB multimer entry:
pLDDT · ipTM · ipSAE · pDockQ2 · LIS 👇
youtu.be/k4yBqddtPyQ
#AlphaFold #AFDB
The AlphaFold-Multimer prediction for your protein looks great. But how confident should you actually be in it?
Razan Abbara breaks down the 5 confidence metrics behind every AFDB multimer entry:
pLDDT · ipTM · ipSAE · pDockQ2 · LIS 👇
youtu.be/k4yBqddtPyQ
#AlphaFold #AFDB
September 3, 2026 at 12:26 PM
New video 🎥
The AlphaFold-Multimer prediction for your protein looks great. But how confident should you actually be in it?
Razan Abbara breaks down the 5 confidence metrics behind every AFDB multimer entry:
pLDDT · ipTM · ipSAE · pDockQ2 · LIS 👇
youtu.be/k4yBqddtPyQ
#AlphaFold #AFDB
The AlphaFold-Multimer prediction for your protein looks great. But how confident should you actually be in it?
Razan Abbara breaks down the 5 confidence metrics behind every AFDB multimer entry:
pLDDT · ipTM · ipSAE · pDockQ2 · LIS 👇
youtu.be/k4yBqddtPyQ
#AlphaFold #AFDB
Truly honored that our work was highlighted as one of many applications where #Alphafold has had an enormous impact
December 9, 2024 at 5:13 PM
Truly honored that our work was highlighted as one of many applications where #Alphafold has had an enormous impact
I just started this alphafold multimer run. Looks like it's running. First time. I am excited.
January 21, 2025 at 2:43 PM
I just started this alphafold multimer run. Looks like it's running. First time. I am excited.
Then came Chai-1, a quiet revolution in structure prediction.
Unlike AlphaFold-Multimer, Chai-1:
✅ Doesn’t need MSAs
✅ Outperforms with single sequences
✅ Predicts multimer structures at AlphaFold-level accuracy
One model, less data, more power.
Unlike AlphaFold-Multimer, Chai-1:
✅ Doesn’t need MSAs
✅ Outperforms with single sequences
✅ Predicts multimer structures at AlphaFold-level accuracy
One model, less data, more power.
April 18, 2025 at 10:30 AM
Then came Chai-1, a quiet revolution in structure prediction.
Unlike AlphaFold-Multimer, Chai-1:
✅ Doesn’t need MSAs
✅ Outperforms with single sequences
✅ Predicts multimer structures at AlphaFold-level accuracy
One model, less data, more power.
Unlike AlphaFold-Multimer, Chai-1:
✅ Doesn’t need MSAs
✅ Outperforms with single sequences
✅ Predicts multimer structures at AlphaFold-level accuracy
One model, less data, more power.
Nice resource! #AlphaFold #PPI #ProteinInteractions
Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions: Molecular Cell www.cell.com/molecular-ce...
Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions: Molecular Cell www.cell.com/molecular-ce...
Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions
Schmid and Walter train a classifier that discerns functionally relevant structure
predictions in proteome-wide protein-protein interaction (PPI) screens using AlphaFold-Multimer,
and they use this co...
www.cell.com
February 26, 2025 at 8:14 PM
Nice resource! #AlphaFold #PPI #ProteinInteractions
Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions: Molecular Cell www.cell.com/molecular-ce...
Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions: Molecular Cell www.cell.com/molecular-ce...
AlphaFold2-WebGPU now supports AlphaFold-Multimer. As in ColabFold, simply use : to separate chains in the sequence input. It is also becoming much more stable: I was able to predict a 491-aa protein in ~4 minutes in M4 Pro. Chrome currently performs better than Firefox for WebGPU, unfortunately.
Run AlphaFold2 locally in your browser via WebGPU, no installation needed, it's just a static webpage using your own GPU or CPU. Short proteins run in seconds. Larger ones are still slow: a 291-aa protein takes ~7 minutes on my M4 Pro.
❗It's just a PoC.
🌐 martin-steinegger.github.io/alphafold2-w...
❗It's just a PoC.
🌐 martin-steinegger.github.io/alphafold2-w...
September 2, 2026 at 5:36 PM
AlphaFold2-WebGPU now supports AlphaFold-Multimer. As in ColabFold, simply use : to separate chains in the sequence input. It is also becoming much more stable: I was able to predict a 491-aa protein in ~4 minutes in M4 Pro. Chrome currently performs better than Firefox for WebGPU, unfortunately.
Viral immune evasion proteins are widespread and block both bacterial and human immune proteins! Go check out Erez’s paper using AlphaFold-multimer to screen for new anti-defense proteins!!🤩🤩
I'm thrilled to announce our latest work is now published in Cell! Viruses encode numerous proteins that inhibit host defenses, but identifying immune-modulatory proteins among millions of viral sequences has been nearly impossible - until now! www.cell.com/cell/fulltex...
January 23, 2025 at 8:46 PM
Viral immune evasion proteins are widespread and block both bacterial and human immune proteins! Go check out Erez’s paper using AlphaFold-multimer to screen for new anti-defense proteins!!🤩🤩
How cool is that! Thank you to @demishassabis.bsky.social and John Jumper for highlighting our #AlphaFold use to gain molecular insights into the mechanism of fertilization in interviews and even your #NobelLecture! Interested in reading more? Check out our paper! www.cell.com/cell/fulltex...
December 9, 2024 at 3:53 PM
How cool is that! Thank you to @demishassabis.bsky.social and John Jumper for highlighting our #AlphaFold use to gain molecular insights into the mechanism of fertilization in interviews and even your #NobelLecture! Interested in reading more? Check out our paper! www.cell.com/cell/fulltex...
Alphafold Multimer creation of fission yeast Gef2-Nod1 interaction via their C-termini!
November 22, 2024 at 6:43 PM
Alphafold Multimer creation of fission yeast Gef2-Nod1 interaction via their C-termini!
Nature featured work from our Pauli lab, where AlphaFold-Multimer helped reveal how Tmem81 and two sperm proteins create the pocket for the egg protein Bouncer to bind.
Andrea Pauli: “AlphaFold speeds up discovery, we use it for every project.”
🔗 www.nature.com/articles/d41...
Andrea Pauli: “AlphaFold speeds up discovery, we use it for every project.”
🔗 www.nature.com/articles/d41...
AlphaFold is five years old — these charts show how it revolutionized science
Since it was unveiled in 2020, Google DeepMind's game-changing AI tool has helped researchers all over the world to predict the 3D structures of hundreds of millions of proteins.
www.nature.com
November 27, 2025 at 1:04 PM
Nature featured work from our Pauli lab, where AlphaFold-Multimer helped reveal how Tmem81 and two sperm proteins create the pocket for the egg protein Bouncer to bind.
Andrea Pauli: “AlphaFold speeds up discovery, we use it for every project.”
🔗 www.nature.com/articles/d41...
Andrea Pauli: “AlphaFold speeds up discovery, we use it for every project.”
🔗 www.nature.com/articles/d41...
Online Now: Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions Online now:
Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions
Schmid and Walter train a classifier that discerns functionally relevant structure predictions in proteome-wide protein-protein interaction (PPI) screens using AlphaFold-Multimer, and they use this confidence metric to curate a database of 40,000…
dlvr.it
February 26, 2025 at 11:57 PM
Online Now: Predictomes, a classifier-curated database of AlphaFold-modeled protein-protein interactions Online now:
Comprehensive Evaluation of AlphaFold-Multimer, AlphaFold3 and ColabFold, and Scoring Functions in Predicting Protein-Peptide Complex Structures https://www.biorxiv.org/content/10.1101/2024.11.11.622992v1
Comprehensive Evaluation of AlphaFold-Multimer, AlphaFold3 and ColabFold, and Scoring Functions in Predicting Protein-Peptide Complex Structures https://www.biorxiv.org/content/10.1101/2024.11.11.622992v1
Determining the three-dimensional structures of protein-peptide complexes is crucial for elucidating
www.biorxiv.org
November 12, 2024 at 3:46 AM
Comprehensive Evaluation of AlphaFold-Multimer, AlphaFold3 and ColabFold, and Scoring Functions in Predicting Protein-Peptide Complex Structures https://www.biorxiv.org/content/10.1101/2024.11.11.622992v1
In silico discovery of nanobody binders to a G-protein coupled receptor using AlphaFold-Multimer https://www.biorxiv.org/content/10.1101/2025.03.05.640882v1
March 10, 2025 at 5:45 PM
In silico discovery of nanobody binders to a G-protein coupled receptor using AlphaFold-Multimer https://www.biorxiv.org/content/10.1101/2025.03.05.640882v1
“AFM-RL: Large Protein Complex Docking Using AlphaFold-Multimer and Reinforcement Learning”
doi.org/10.1101/2024.01.20.576386
doi.org/10.1101/2024.01.20.576386
January 24, 2024 at 6:37 AM
“AFM-RL: Large Protein Complex Docking Using AlphaFold-Multimer and Reinforcement Learning”
doi.org/10.1101/2024.01.20.576386
doi.org/10.1101/2024.01.20.576386
“SpatialPPI: three-dimensional space protein-protein interaction prediction with AlphaFold Multimer”
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 16, 2023 at 2:00 PM
“SpatialPPI: three-dimensional space protein-protein interaction prediction with AlphaFold Multimer”
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
New Title Alert: af_analysis- is a Python package for analysis of AlphaFold protein structure predictions from AlphaFold 2/3, ColabFold, AlphaFold-Multimer, AlphaPulldown, Boltz1, Chai-1, and MassiveFold.
Learn more here: buff.ly/BeBrAei
#SBGrid #Software #Analysis
Learn more here: buff.ly/BeBrAei
#SBGrid #Software #Analysis
GitHub - samuelmurail/af_analysis: Analysis of alphafold and colabfold results
Analysis of alphafold and colabfold results. Contribute to samuelmurail/af_analysis development by creating an account on GitHub.
buff.ly
May 12, 2026 at 5:58 PM
New Title Alert: af_analysis- is a Python package for analysis of AlphaFold protein structure predictions from AlphaFold 2/3, ColabFold, AlphaFold-Multimer, AlphaPulldown, Boltz1, Chai-1, and MassiveFold.
Learn more here: buff.ly/BeBrAei
#SBGrid #Software #Analysis
Learn more here: buff.ly/BeBrAei
#SBGrid #Software #Analysis
Btw check out our collaborative effort with the Walter Lab to map nucleosome acidic patch interactors for all nuclear proteins: predictomes.org/view/acidicp...
Predictomes | H. sapiens H2A/H2B vs. nuclear proteome
A free interactive resource for viewing predicted AlphaFold multimer structures for protein pairs in biological pathways.
predictomes.org
November 15, 2024 at 3:43 PM
Btw check out our collaborative effort with the Walter Lab to map nucleosome acidic patch interactors for all nuclear proteins: predictomes.org/view/acidicp...
Enter PHLEGM! 💻🧬 We developed the Phage Homomer Level Estimate and Generation Method to infer oligomeric state using AlphaFold-Multimer and interface quality assessment. We applied it to >22,000 sequences, revealing massive structural diversity. (2/n)
May 26, 2026 at 4:34 PM
Enter PHLEGM! 💻🧬 We developed the Phage Homomer Level Estimate and Generation Method to infer oligomeric state using AlphaFold-Multimer and interface quality assessment. We applied it to >22,000 sequences, revealing massive structural diversity. (2/n)
TIL Rosetta is an LLM
(but that mistake aside, this is a nice op-ed about how pretraining is taking over computational biology)
(but that mistake aside, this is a nice op-ed about how pretraining is taking over computational biology)
February 4, 2025 at 10:36 AM
TIL Rosetta is an LLM
(but that mistake aside, this is a nice op-ed about how pretraining is taking over computational biology)
(but that mistake aside, this is a nice op-ed about how pretraining is taking over computational biology)