Major modes of behavior within low-pLDDT regions were identified through a survey of human proteome predictions provided by the AlphaFold Protein Structure Database #AlphaFold2 #StructurePrediction #ConditionalFolding doi.org/10.1107/S205...
October 20, 2025 at 12:43 PM
Major modes of behavior within low-pLDDT regions were identified through a survey of human proteome predictions provided by the AlphaFold Protein Structure Database #AlphaFold2 #StructurePrediction #ConditionalFolding doi.org/10.1107/S205...
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...
Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation
doi.org/10.1101/2025...
October 7, 2025 at 9:20 PM
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...
Martin Grønbæk-Thygesen (from @rhp-lab.bsky.social) et al show that introducing K here causes ubiquitylation and degradation
doi.org/10.1101/2025...
With the 2025 Nobel Prize in Chemistry being announced tomorrow, here's a reminder of the research on protein structure prediction that won last year's prize: www.compoundchem.com/2024/10/10/2...
#ChemSky 🧪
#ChemSky 🧪
October 7, 2025 at 4:32 PM
With the 2025 Nobel Prize in Chemistry being announced tomorrow, here's a reminder of the research on protein structure prediction that won last year's prize: www.compoundchem.com/2024/10/10/2...
#ChemSky 🧪
#ChemSky 🧪
BindCraft: an AlphaFold2-powered de novo protein binder design tool 🧬✨
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
One-shot design of functional protein binders with BindCraft - Nature
BindCraft, an open-source, automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity without the need for high-throughput screening.
www.nature.com
October 5, 2025 at 12:07 PM
BindCraft: an AlphaFold2-powered de novo protein binder design tool 🧬✨
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
October issue is now available! journals.iucr.org/d/issues/202...
The cover highlights the article on categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures from the Richardson lab @duke-university.bsky.social : doi.org/10.1107/S205...
Image credit: Chistopher Williams
The cover highlights the article on categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures from the Richardson lab @duke-university.bsky.social : doi.org/10.1107/S205...
Image credit: Chistopher Williams
October 2, 2025 at 1:58 PM
October issue is now available! journals.iucr.org/d/issues/202...
The cover highlights the article on categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures from the Richardson lab @duke-university.bsky.social : doi.org/10.1107/S205...
Image credit: Chistopher Williams
The cover highlights the article on categorizing prediction modes within low-pLDDT regions of AlphaFold2 structures from the Richardson lab @duke-university.bsky.social : doi.org/10.1107/S205...
Image credit: Chistopher Williams
I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign
doi.org/10.1101/2025.09.24.678028 #proteindesign
September 28, 2025 at 9:16 PM
I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5)
doi.org/10.1101/2025.09.24.678028 #proteindesign
doi.org/10.1101/2025.09.24.678028 #proteindesign
Anecdotal experience with AlphaFold3 vs AlphaFold2:
The pLDDT, ipTM, and pTM scores are constantly scoring worse than the same input in AF2, but the PAE is better with AF3.
Anyone else have the same experience?
The pLDDT, ipTM, and pTM scores are constantly scoring worse than the same input in AF2, but the PAE is better with AF3.
Anyone else have the same experience?
September 21, 2024 at 3:56 AM
Anecdotal experience with AlphaFold3 vs AlphaFold2:
The pLDDT, ipTM, and pTM scores are constantly scoring worse than the same input in AF2, but the PAE is better with AF3.
Anyone else have the same experience?
The pLDDT, ipTM, and pTM scores are constantly scoring worse than the same input in AF2, but the PAE is better with AF3.
Anyone else have the same experience?
Unsupervised domain classification of AlphaFold2-predicted protein structures https://www.biorxiv.org/content/10.1101/2024.08.21.608992v1
Unsupervised domain classification of AlphaFold2-predicted protein structures https://www.biorxiv.org/content/10.1101/2024.08.21.608992v1
The release of the AlphaFold database, which contains 214 million predicted protein structures, repr
www.biorxiv.org
August 22, 2024 at 3:47 AM
Unsupervised domain classification of AlphaFold2-predicted protein structures https://www.biorxiv.org/content/10.1101/2024.08.21.608992v1
Even as of last January, people were using AF2 to sample multiple conformations. He says in the abstract -- "Here, I argue that AlphaFold2 and its peers are currently limited by the fact that they predict only a single structure." Straw man argument - wrong then, wrong now.
November 5, 2023 at 3:02 AM
Even as of last January, people were using AF2 to sample multiple conformations. He says in the abstract -- "Here, I argue that AlphaFold2 and its peers are currently limited by the fact that they predict only a single structure." Straw man argument - wrong then, wrong now.
AlphaFold2 knows some protein folding principles https://www.biorxiv.org/content/10.1101/2024.08.25.609581v1
AlphaFold2 knows some protein folding principles https://www.biorxiv.org/content/10.1101/2024.08.25.609581v1
AlphaFold2 (AF2) has revolutionized protein structure prediction. However, a common confusion lies i
www.biorxiv.org
August 26, 2024 at 5:48 PM
AlphaFold2 knows some protein folding principles https://www.biorxiv.org/content/10.1101/2024.08.25.609581v1
📃Scientific paper: Accuracy of a machine learning method based on structural and locational information from AlphaFold2 for predicting the pathogenicity of TARDBP and FUS gene variants in ALS
Ref.: BioMed Central, 2023
➡️ Continued on ES/IODE
Ref.: BioMed Central, 2023
➡️ Continued on ES/IODE
January 9, 2025 at 6:02 PM
📃Scientific paper: Accuracy of a machine learning method based on structural and locational information from AlphaFold2 for predicting the pathogenicity of TARDBP and FUS gene variants in ALS
Ref.: BioMed Central, 2023
➡️ Continued on ES/IODE
Ref.: BioMed Central, 2023
➡️ Continued on ES/IODE
The bioweapon may not be control by what ever maybe control similar nemesys3 similar resident evil3 but not what ever protein bio chips, bio antennas? AlphaFold2 + tech? www.youtube.com/watch?v=TQMB... www.youtube.com/watch?v=Uz7u...
Webconference: De los wearables a los biochips
YouTube video by OBS Business School
www.youtube.com
January 26, 2025 at 2:17 AM
The bioweapon may not be control by what ever maybe control similar nemesys3 similar resident evil3 but not what ever protein bio chips, bio antennas? AlphaFold2 + tech? www.youtube.com/watch?v=TQMB... www.youtube.com/watch?v=Uz7u...
Ophthopedia Update: Deep learning-based assessment of missense variants in the COG4 gene presented with bilateral congenital cataract: Objective
We compared the protein structure and pathogenicity of clinically relevant variants of the COG4 gene with AlphaFold2 (AF2), Alpha Missense (AM), and…
We compared the protein structure and pathogenicity of clinically relevant variants of the COG4 gene with AlphaFold2 (AF2), Alpha Missense (AM), and…
Deep learning-based assessment of missense variants in the COG4 gene presented with bilateral congenital cataract
Objective
We compared the protein structure and pathogenicity of clinically relevant variants of the COG4 gene with AlphaFold2 (AF2), Alpha Missense (AM), and ThermoMPNN for the first time.
Methods and analysis
The sequences of clinically relevant…
dlvr.it
January 14, 2025 at 10:41 AM
Ophthopedia Update: Deep learning-based assessment of missense variants in the COG4 gene presented with bilateral congenital cataract: Objective
We compared the protein structure and pathogenicity of clinically relevant variants of the COG4 gene with AlphaFold2 (AF2), Alpha Missense (AM), and…
We compared the protein structure and pathogenicity of clinically relevant variants of the COG4 gene with AlphaFold2 (AF2), Alpha Missense (AM), and…
'Predicting multiple conformations via sequence clustering and AlphaFold2' www.nature.com/articles/s41...
cellmolbiocommunity.springernature.com/posts/predic...
Pretty cool seeing this (sort of) published. I watched this seminar about it a few months ago and was blown away:
youtu.be/rgGceDDnIEo?...
cellmolbiocommunity.springernature.com/posts/predic...
Pretty cool seeing this (sort of) published. I watched this seminar about it a few months ago and was blown away:
youtu.be/rgGceDDnIEo?...
Understanding & discovering fold-switching proteins by combining AlphaFold2 & sequence clustering
Presented on April 12th 2023 by Hannah Wayment-Steele
youtu.be
November 13, 2023 at 10:16 PM
'Predicting multiple conformations via sequence clustering and AlphaFold2' www.nature.com/articles/s41...
cellmolbiocommunity.springernature.com/posts/predic...
Pretty cool seeing this (sort of) published. I watched this seminar about it a few months ago and was blown away:
youtu.be/rgGceDDnIEo?...
cellmolbiocommunity.springernature.com/posts/predic...
Pretty cool seeing this (sort of) published. I watched this seminar about it a few months ago and was blown away:
youtu.be/rgGceDDnIEo?...
🔬 How does #AlphaFold2 perform with minimal sequence input?
"Dissecting AlphaFold2’s capabilities with limited sequence information" reveals insights into its ability to predict #ProteinStructures using structural templates without deep MSAs.
Read more: doi.org/10.1093/bioa...
"Dissecting AlphaFold2’s capabilities with limited sequence information" reveals insights into its ability to predict #ProteinStructures using structural templates without deep MSAs.
Read more: doi.org/10.1093/bioa...
December 19, 2024 at 2:40 PM
🔬 How does #AlphaFold2 perform with minimal sequence input?
"Dissecting AlphaFold2’s capabilities with limited sequence information" reveals insights into its ability to predict #ProteinStructures using structural templates without deep MSAs.
Read more: doi.org/10.1093/bioa...
"Dissecting AlphaFold2’s capabilities with limited sequence information" reveals insights into its ability to predict #ProteinStructures using structural templates without deep MSAs.
Read more: doi.org/10.1093/bioa...
contrast to the later end-to-end architectures of AlphaFold2 and AlphaFold3. While this potential was originally justified by referring to physical potentials of mean force (PMFs), we reinterpret AlphaFold1's potential as an instance of probability [2/7 of https://arxiv.org/abs/2505.19763v1]
May 27, 2025 at 6:51 AM
contrast to the later end-to-end architectures of AlphaFold2 and AlphaFold3. While this potential was originally justified by referring to physical potentials of mean force (PMFs), we reinterpret AlphaFold1's potential as an instance of probability [2/7 of https://arxiv.org/abs/2505.19763v1]
'When the Protein Data Bank opened, it held the structures of seven proteins. By the time Google DeepMind used it to train AlphaFold2 nearly 50 years later, it held more than 140,000 — each laboriously decoded by the scientists known as structural biologists.'
www.quantamagazine.org/how-ai-revol...
www.quantamagazine.org/how-ai-revol...
How AI Revolutionized Protein Science, but Didn’t End It | Quanta Magazine
Three years ago, Google’s AlphaFold pulled off the biggest artificial intelligence breakthrough in science to date, accelerating molecular research and kindling deep questions about why we do science.
www.quantamagazine.org
May 15, 2025 at 2:12 PM
'When the Protein Data Bank opened, it held the structures of seven proteins. By the time Google DeepMind used it to train AlphaFold2 nearly 50 years later, it held more than 140,000 — each laboriously decoded by the scientists known as structural biologists.'
www.quantamagazine.org/how-ai-revol...
www.quantamagazine.org/how-ai-revol...
The results show that AlphaFold3 slightly outperforms AlphaFold2 for protein complexes, but the difference disappears when extensive sampling is applied to AlphaFold2. The AF3-server performs better than AlphaFold2 for easier targets, but not for harder ones.
September 23, 2025 at 4:45 PM
The results show that AlphaFold3 slightly outperforms AlphaFold2 for protein complexes, but the difference disappears when extensive sampling is applied to AlphaFold2. The AF3-server performs better than AlphaFold2 for easier targets, but not for harder ones.
IMPROVING ALPHAFOLD2 PERFORMANCE WITH A GLOBAL METAGENOMIC & BIOLOGICAL DATA SUPPLY CHAIN https://www.biorxiv.org/content/10.1101/2024.03.06.583325v1
IMPROVING ALPHAFOLD2 PERFORMANCE WITH A GLOBAL METAGENOMIC & BIOLOGICAL DATA SUPPLY CHAIN https://www.biorxiv.org/content/10.1101/2024.03.06.583325v1
Scaling laws suggest that more than a trillion species inhabit our planet but only a miniscule and u
www.biorxiv.org
March 7, 2024 at 3:34 AM
IMPROVING ALPHAFOLD2 PERFORMANCE WITH A GLOBAL METAGENOMIC & BIOLOGICAL DATA SUPPLY CHAIN https://www.biorxiv.org/content/10.1101/2024.03.06.583325v1
As an example, Jumper et al 2021 introduced AlphaFold2, and had 28,975 google scholar citations as of today. They also won a Nobel prize. So some tools get rewarded by peers I guess :)
November 21, 2024 at 2:11 PM
As an example, Jumper et al 2021 introduced AlphaFold2, and had 28,975 google scholar citations as of today. They also won a Nobel prize. So some tools get rewarded by peers I guess :)
Applicability of AlphaFold2 in the modelling of coiled-coil domains www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
March 11, 2024 at 9:00 AM
Applicability of AlphaFold2 in the modelling of coiled-coil domains www.biorxiv.org/cont...
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#proteomics #prot-preprint
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#proteomics #prot-preprint
gapTrick - Structural characterisation of protein-protein interactions using AlphaFold with multimeric templates [new]
AlphaFold2 refines protein complex models via multimeric templates, enhancing weak contact prediction.
AlphaFold2 refines protein complex models via multimeric templates, enhancing weak contact prediction.
February 6, 2025 at 6:26 PM
gapTrick - Structural characterisation of protein-protein interactions using AlphaFold with multimeric templates [new]
AlphaFold2 refines protein complex models via multimeric templates, enhancing weak contact prediction.
AlphaFold2 refines protein complex models via multimeric templates, enhancing weak contact prediction.
We are at the inauguration of #ISMBECCB2025 Liverpool UK! Let’s begin with a fantastic keynote speaker! John Jumper, Nobel Prize dinner for the work with Google Deep Mind and #alphafold2
#proteins #structure #prediction #bioinformatics #ISMBECCB2025 #iscbsc
#proteins #structure #prediction #bioinformatics #ISMBECCB2025 #iscbsc
July 20, 2025 at 6:27 PM
We are at the inauguration of #ISMBECCB2025 Liverpool UK! Let’s begin with a fantastic keynote speaker! John Jumper, Nobel Prize dinner for the work with Google Deep Mind and #alphafold2
#proteins #structure #prediction #bioinformatics #ISMBECCB2025 #iscbsc
#proteins #structure #prediction #bioinformatics #ISMBECCB2025 #iscbsc
⭐️ EDITOR'S CHOICE ⭐️
Hand-picked by our Editor-in-Chief as the stand-out article in the issue.
🔦🌱 RESEARCH 🌱🔦
"The nuclear sulfenome of Arabidopsis: spotlight on histone acetyltransferase GCN5 regulation through functional thiols" – De Smet et al. doi.org/10.1093/jxb/...
#PlantScience 🧪
Hand-picked by our Editor-in-Chief as the stand-out article in the issue.
🔦🌱 RESEARCH 🌱🔦
"The nuclear sulfenome of Arabidopsis: spotlight on histone acetyltransferase GCN5 regulation through functional thiols" – De Smet et al. doi.org/10.1093/jxb/...
#PlantScience 🧪
April 30, 2025 at 11:25 AM
⭐️ EDITOR'S CHOICE ⭐️
Hand-picked by our Editor-in-Chief as the stand-out article in the issue.
🔦🌱 RESEARCH 🌱🔦
"The nuclear sulfenome of Arabidopsis: spotlight on histone acetyltransferase GCN5 regulation through functional thiols" – De Smet et al. doi.org/10.1093/jxb/...
#PlantScience 🧪
Hand-picked by our Editor-in-Chief as the stand-out article in the issue.
🔦🌱 RESEARCH 🌱🔦
"The nuclear sulfenome of Arabidopsis: spotlight on histone acetyltransferase GCN5 regulation through functional thiols" – De Smet et al. doi.org/10.1093/jxb/...
#PlantScience 🧪