_machine
@machine-etal.bsky.social
Ph.D. / Protein Science / Apptainer (Singularity) おじさん / フォローはお気軽に🥳 / My posts and opinions are my own🙃
Reposted by _machine
AmberTools 25 is now available on Homebrew🎉
brew install brewsci/bio/ambertools
brew install brewsci/bio/ambertools
December 20, 2025 at 4:33 PM
AmberTools 25 is now available on Homebrew🎉
brew install brewsci/bio/ambertools
brew install brewsci/bio/ambertools
Reposted by _machine
Our review on Integrative modelling of biomolecular dynamics 💃 is now live at COSB
We discuss approaches to integrate computational methods with time-dependent & time-resolved experiments to study protein dynamics
With @dariagusew.bsky.social & Carl G. Henning Hansen
doi.org/10.1016/j.sb...
We discuss approaches to integrate computational methods with time-dependent & time-resolved experiments to study protein dynamics
With @dariagusew.bsky.social & Carl G. Henning Hansen
doi.org/10.1016/j.sb...
December 9, 2025 at 10:13 PM
Our review on Integrative modelling of biomolecular dynamics 💃 is now live at COSB
We discuss approaches to integrate computational methods with time-dependent & time-resolved experiments to study protein dynamics
With @dariagusew.bsky.social & Carl G. Henning Hansen
doi.org/10.1016/j.sb...
We discuss approaches to integrate computational methods with time-dependent & time-resolved experiments to study protein dynamics
With @dariagusew.bsky.social & Carl G. Henning Hansen
doi.org/10.1016/j.sb...
Reposted by _machine
『エルデンリング ナイトレイン』の新DLCでは「毒沼」とうとう実装へ。“いつの間にか誰かが入れた”毒沼
automaton-media.com/articles/new...
automaton-media.com/articles/new...
December 2, 2025 at 1:47 AM
『エルデンリング ナイトレイン』の新DLCでは「毒沼」とうとう実装へ。“いつの間にか誰かが入れた”毒沼
automaton-media.com/articles/new...
automaton-media.com/articles/new...
Papier-mâché Suica Penguin, the Japanese railway character—made like a matryoshka doll 🐧
December 1, 2025 at 3:46 PM
Papier-mâché Suica Penguin, the Japanese railway character—made like a matryoshka doll 🐧
Reposted by _machine
Been excited about this one for a while! What would you do with a new alphabet and the wealth of protein sequence bioinformatics at your disposal? We're also around at #EMBOComp3D Heidelberg and MLSB Copenhagen this week to discuss
Fresh from bioRxiv our latest work introducing The Embedded Alphabet (TEA), a powerful new representation for protein sequences obtained by discretising ESM2 embeddings into 20 characters.
Pre-print: www.biorxiv.org/content/10.1...
🧵👇(1/n)
Pre-print: www.biorxiv.org/content/10.1...
🧵👇(1/n)
Rewriting protein alphabets with language models
Detecting remote homology with speed and sensitivity is crucial for tasks like function annotation and structure prediction. We introduce a novel approach using contrastive learning to convert protein...
www.biorxiv.org
December 1, 2025 at 10:58 AM
Been excited about this one for a while! What would you do with a new alphabet and the wealth of protein sequence bioinformatics at your disposal? We're also around at #EMBOComp3D Heidelberg and MLSB Copenhagen this week to discuss
Swapped my silent linear switches to regular linears for my home setup, and upgraded the keycaps to a PBS profile while I was at it. 🫐🫐🫐
November 30, 2025 at 1:49 PM
Swapped my silent linear switches to regular linears for my home setup, and upgraded the keycaps to a PBS profile while I was at it. 🫐🫐🫐
People say de novo antibody design lets you target any epitope, but I doubt it. Antibody topology can’t cover all protein surfaces, and PDB-trained methods narrow that space even more.
November 29, 2025 at 7:36 AM
People say de novo antibody design lets you target any epitope, but I doubt it. Antibody topology can’t cover all protein surfaces, and PDB-trained methods narrow that space even more.
Reposted by _machine
Reliable Identification of Homodimers Using AlphaFold https://www.biorxiv.org/content/10.1101/2025.11.27.691011v1
November 28, 2025 at 2:46 AM
Reliable Identification of Homodimers Using AlphaFold https://www.biorxiv.org/content/10.1101/2025.11.27.691011v1
Reposted by _machine
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
biorxiv.org
November 12, 2025 at 9:26 PM
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Reposted by _machine
A few py2Dmol updates 🧬
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
November 19, 2025 at 8:15 AM
A few py2Dmol updates 🧬
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
Reposted by _machine
This paper has been published in ACS Omega: pubs.acs.org/doi/10.1021/...
Available at Google Colaboratory: github.com/cddlab/colab...
Available at Google Colaboratory: github.com/cddlab/colab...
November 10, 2025 at 5:56 AM
This paper has been published in ACS Omega: pubs.acs.org/doi/10.1021/...
Available at Google Colaboratory: github.com/cddlab/colab...
Available at Google Colaboratory: github.com/cddlab/colab...
Reposted by _machine
UniProt is changing its reference proteomes resource.
Reference proteomes will remain in UniProtKB, while others will move to UniParc.
Read more about these changes:
www.ebi.ac.uk/about/news/u...
🧬 🖥️
Uniprot is a collaboration between EMBL-EBI, @sib.swiss & the Protein Information Resource.
Reference proteomes will remain in UniProtKB, while others will move to UniParc.
Read more about these changes:
www.ebi.ac.uk/about/news/u...
🧬 🖥️
Uniprot is a collaboration between EMBL-EBI, @sib.swiss & the Protein Information Resource.
Changes to UniProt proteomes
UniProt, the data resource for protein sequence and function information, is making major changes to its proteomes resource and to the UniProt Knowledgebase. UniProt has developed a new workflow that ...
www.ebi.ac.uk
November 4, 2025 at 9:58 AM
UniProt is changing its reference proteomes resource.
Reference proteomes will remain in UniProtKB, while others will move to UniParc.
Read more about these changes:
www.ebi.ac.uk/about/news/u...
🧬 🖥️
Uniprot is a collaboration between EMBL-EBI, @sib.swiss & the Protein Information Resource.
Reference proteomes will remain in UniProtKB, while others will move to UniParc.
Read more about these changes:
www.ebi.ac.uk/about/news/u...
🧬 🖥️
Uniprot is a collaboration between EMBL-EBI, @sib.swiss & the Protein Information Resource.
Reposted by _machine
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
October 28, 2025 at 6:30 PM
OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇
Reposted by _machine
Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...
GitHub - aqlaboratory/openfold-3: OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3
OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3 - aqlaboratory/openfold-3
github.com
October 28, 2025 at 9:30 AM
Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...
Reposted by _machine
Now DSSP 4.5.6 and its python module are available on Homebrew. `brew install brewsci/bio/dssp`.
> Since version 4.5.2 it is possible to build a Python module to directly work with DSSP info inside your Python scripts.
github.com/PDB-REDO/dssp
It can be installed using `brew install brewsci/bio/dssp`. I hope it will also be available on PyPI.
github.com/PDB-REDO/dssp
It can be installed using `brew install brewsci/bio/dssp`. I hope it will also be available on PyPI.
GitHub - PDB-REDO/dssp: Application to assign secondary structure to proteins
Application to assign secondary structure to proteins - PDB-REDO/dssp
github.com
October 28, 2025 at 5:48 AM
Now DSSP 4.5.6 and its python module are available on Homebrew. `brew install brewsci/bio/dssp`.
Reposted by _machine
Our new preprint is out. Our group performed a comprehensive protein–protein complex prediction within 2,437 biosynthetic gene clusters. We predicted a total of 487,828 complexes for known BGCs, identifying 15,438 heteromeric interactions with an ipTM ≥ 0.6. (2/3)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Predicting protein complexes in biosynthetic gene clusters
Biosynthetic gene clusters (BGCs) are contiguous genomic regions that encode diverse, non-homologous proteins required for the production of specific natural products. Their genetic diversity underlie...
www.biorxiv.org
October 28, 2025 at 5:58 AM
Our new preprint is out. Our group performed a comprehensive protein–protein complex prediction within 2,437 biosynthetic gene clusters. We predicted a total of 487,828 complexes for known BGCs, identifying 15,438 heteromeric interactions with an ipTM ≥ 0.6. (2/3)
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by _machine
We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵
October 23, 2025 at 1:08 PM
We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵
Reposted by _machine
End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio
🌐 evedesign.bio
October 22, 2025 at 2:30 PM
End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio
🌐 evedesign.bio
Reposted by _machine
Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...
blog.genesmindsmachines.com/p/we-still-c...
We still can’t predict much of anything in biology
Biology is hard. Yes, even for AI.
blog.genesmindsmachines.com
October 7, 2025 at 4:11 PM
Biology is much more complicated than most non-biologists can imagine. And AI is not going to change this anytime soon.
blog.genesmindsmachines.com/p/we-still-c...
blog.genesmindsmachines.com/p/we-still-c...
Reposted by _machine
We thank reviewer 2 for their constructive suggestions and have updated our manuscript accordingly
October 15, 2025 at 10:42 PM
We thank reviewer 2 for their constructive suggestions and have updated our manuscript accordingly
Cornix届いてました。これはエンドゲーム感あるねえ
October 14, 2025 at 10:38 AM
Cornix届いてました。これはエンドゲーム感あるねえ
Reposted by _machine
New job! Senior scientist in AI/ML at Takeda. The plan is to do some fun stuff with biomolecular foundation models
October 13, 2025 at 8:59 PM
New job! Senior scientist in AI/ML at Takeda. The plan is to do some fun stuff with biomolecular foundation models
Reposted by _machine
Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
September 26, 2025 at 2:28 AM
Initial attempt at replicating in relion (parameters in next post). This is for Aca2-RNA, using a 100k subset of the 2D-classified particles (no prior 3D cleanup).
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.
A 1-class ab initio in relion, then local refinement in relion (1.8deg searches+blush) gives a nominally 3.3Å map; 3.5 Å w/out blush.