_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
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.
Reposted by _machine
September 24, 2025 at 2:31 PM
Reposted by _machine
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
Reposted by _machine
pip install ipsae
from www.linkedin.com/in/ullah-sam...
www.youtube.com/watch?v=A5ph...
PyPI pypi.org/project/ipsae/
His github fork github.com/ullahsamee/I...
My github github.com/DunbrackLab/...
Paper www.biorxiv.org/content/10.1...
For designed protein binders www.biorxiv.org/content/10.1...
from www.linkedin.com/in/ullah-sam...
www.youtube.com/watch?v=A5ph...
PyPI pypi.org/project/ipsae/
His github fork github.com/ullahsamee/I...
My github github.com/DunbrackLab/...
Paper www.biorxiv.org/content/10.1...
For designed protein binders www.biorxiv.org/content/10.1...
Screen binders using ipSAE
YouTube video by ProteinDesignStudio
www.youtube.com
September 16, 2025 at 7:21 PM
pip install ipsae
from www.linkedin.com/in/ullah-sam...
www.youtube.com/watch?v=A5ph...
PyPI pypi.org/project/ipsae/
His github fork github.com/ullahsamee/I...
My github github.com/DunbrackLab/...
Paper www.biorxiv.org/content/10.1...
For designed protein binders www.biorxiv.org/content/10.1...
from www.linkedin.com/in/ullah-sam...
www.youtube.com/watch?v=A5ph...
PyPI pypi.org/project/ipsae/
His github fork github.com/ullahsamee/I...
My github github.com/DunbrackLab/...
Paper www.biorxiv.org/content/10.1...
For designed protein binders www.biorxiv.org/content/10.1...
Reposted by _machine
An analysis of scaling laws in paired antibody LMs, which mostly learn the composition of germline sequences. Authors conclude that an 650M parameter NN (the sweet spot for generalist PLMs) would require 5.5 M sequences, about ~3x what is publicly available today www.biorxiv.org/content/10.1...
September 8, 2025 at 11:43 AM
An analysis of scaling laws in paired antibody LMs, which mostly learn the composition of germline sequences. Authors conclude that an 650M parameter NN (the sweet spot for generalist PLMs) would require 5.5 M sequences, about ~3x what is publicly available today www.biorxiv.org/content/10.1...
Reposted by _machine
Preprint: De-novo design of proteins that inhibit bacterial defenses
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection
Bacterial defense systems present considerable barriers to both phage infection and plasmid transformation. These systems target mobile genetic elements, limiting the efficacy of bacteriophage-based t...
www.biorxiv.org
September 2, 2025 at 10:48 AM
Preprint: De-novo design of proteins that inhibit bacterial defenses
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications
Congrats Jeremy Garb!
tinyurl.com/Syttt
🧵
Reposted by _machine
We'll cover our latest work on low resolution applications, a run-through of our codebase, and tutorials of how to run ROCKET on your own data. Join if you're interested!! 🚀
Our monthly software webinars will resume in October with @alisiafadini.bsky.social and @minhuanli.bsky.social covering AlphaFold as a Prior: Guiding Protein Structure Prediction Using Experimental Data with ROCKET.
Tuesday, October 14, 2025 at 12:00pm ET
Register here: buff.ly/uLlQGVr
#SBGrid
Tuesday, October 14, 2025 at 12:00pm ET
Register here: buff.ly/uLlQGVr
#SBGrid
Webinars
The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…
buff.ly
September 2, 2025 at 4:07 PM
We'll cover our latest work on low resolution applications, a run-through of our codebase, and tutorials of how to run ROCKET on your own data. Join if you're interested!! 🚀
Reposted by _machine
August 22, 2025 at 12:20 PM
Reposted by _machine
If you use Boltz1/2, BioEmu, Chai1, or other MSA-dependent models, you’re likely using our ColabFold server. Please be considerate! Avoid large submissions across many IPs instead generate the MSA locally. Our server is an old-timer from 2014 and can’t handle that load.
August 15, 2025 at 5:48 PM
If you use Boltz1/2, BioEmu, Chai1, or other MSA-dependent models, you’re likely using our ColabFold server. Please be considerate! Avoid large submissions across many IPs instead generate the MSA locally. Our server is an old-timer from 2014 and can’t handle that load.
Reposted by _machine
(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Accelerating Biomolecular Modeling with AtomWorks and RF3
Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilita...
www.biorxiv.org
August 15, 2025 at 5:17 PM
(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)
[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)
Reposted by _machine
Fun fact: #bindcraft evolved from a binder design tutorial originally developed for BPDMC!
Come see @martinpacesa.bsky.social tonight at 7pm EDT in Room 181, Building 68, @mit.edu
"BindCraft: one-shot design of functional protein binders"
bpdmc.org
Come see @martinpacesa.bsky.social tonight at 7pm EDT in Room 181, Building 68, @mit.edu
"BindCraft: one-shot design of functional protein binders"
bpdmc.org
schedule
introduction and membership
Boston Protein Design and Modeling Club (BPDMC) is a community of computational protein engineers and modelers from both academia and industry. While we are based in Boston...
bpdmc.org
August 13, 2025 at 1:52 PM
Fun fact: #bindcraft evolved from a binder design tutorial originally developed for BPDMC!
Come see @martinpacesa.bsky.social tonight at 7pm EDT in Room 181, Building 68, @mit.edu
"BindCraft: one-shot design of functional protein binders"
bpdmc.org
Come see @martinpacesa.bsky.social tonight at 7pm EDT in Room 181, Building 68, @mit.edu
"BindCraft: one-shot design of functional protein binders"
bpdmc.org