#proteindesign #proteinbinder
100 designs
⬇️
34 got through the screening (ipTM, PAE, RMSD)
⬇️
4 ordered (gene synthesis + codon optimization)
⬇️
3 expressed and soluble
⬇️
1 interacts with its target !!!!
Now the story begins !
100 designs
⬇️
34 got through the screening (ipTM, PAE, RMSD)
⬇️
4 ordered (gene synthesis + codon optimization)
⬇️
3 expressed and soluble
⬇️
1 interacts with its target !!!!
Now the story begins !
a man with glasses and a mustache is wearing a white shirt and says yes .
ALT: a man with glasses and a mustache is wearing a white shirt and says yes .
media.tenor.com
November 7, 2025 at 12:03 PM
#proteindesign #proteinbinder
100 designs
⬇️
34 got through the screening (ipTM, PAE, RMSD)
⬇️
4 ordered (gene synthesis + codon optimization)
⬇️
3 expressed and soluble
⬇️
1 interacts with its target !!!!
Now the story begins !
100 designs
⬇️
34 got through the screening (ipTM, PAE, RMSD)
⬇️
4 ordered (gene synthesis + codon optimization)
⬇️
3 expressed and soluble
⬇️
1 interacts with its target !!!!
Now the story begins !
I had some problems getting persistent expression of the construct over generations, maybe some silencing. Might need to codon-optimize for the system, or play around with promoters/terminators, but it was definitely initially promising!
November 12, 2025 at 9:10 AM
I had some problems getting persistent expression of the construct over generations, maybe some silencing. Might need to codon-optimize for the system, or play around with promoters/terminators, but it was definitely initially promising!
Methanogenic archaea encoding Pyrrolysine maintain ambiguous amber codon usage
www.pnas.org/doi/10.1073/... #jcampubs
www.pnas.org/doi/10.1073/... #jcampubs
November 7, 2025 at 3:00 PM
Methanogenic archaea encoding Pyrrolysine maintain ambiguous amber codon usage
www.pnas.org/doi/10.1073/... #jcampubs
www.pnas.org/doi/10.1073/... #jcampubs
Methanogenic archaea encoding Pyrrolysine maintain ambiguous amber codon usage | PNAS https://www.pnas.org/doi/abs/10.1073/pnas.2517473122?af=R
Methanogenic archaea encoding Pyrrolysine maintain ambiguous amber codon usage | PNAS
Natural genetic code expansion is a phenomenon wherein an additional amino acid is encoded by a stop codon. These nonstandard amino acids are benef...
www.pnas.org
November 7, 2025 at 12:37 AM
Methanogenic archaea encoding Pyrrolysine maintain ambiguous amber codon usage | PNAS https://www.pnas.org/doi/abs/10.1073/pnas.2517473122?af=R
Next Codon Usage Meeting, May 31st to June 3rd, 2026 in Montreal right after the RNA Society Meeting. The list of speakers will be up soon.
sites.google.com/view/codonus...
sites.google.com/view/codonus...
codon usage
About the Conference
Codon usage bias—the preference for certain synonymous codons—is a key factor in genome regulation. Codon usage and synonymous codon mutations have been shown to influence gene ex...
sites.google.com
November 5, 2025 at 10:55 PM
Next Codon Usage Meeting, May 31st to June 3rd, 2026 in Montreal right after the RNA Society Meeting. The list of speakers will be up soon.
sites.google.com/view/codonus...
sites.google.com/view/codonus...
developer.nvidia.com/blog/introdu...
Will this finally be a codon optimizer that works? Still haven’t ever used a magic bullet but I do know not only the codons but the whole sequence play a big role
Will this finally be a codon optimizer that works? Still haven’t ever used a magic bullet but I do know not only the codons but the whole sequence play a big role
Introducing the CodonFM Open Model for RNA Design and Analysis | NVIDIA Technical Blog
Open research is critical for driving innovation, and many breakthroughs in AI and science are achieved through open collaboration. In the field of digital biology research, NVIDIA Clara supports this...
developer.nvidia.com
October 30, 2025 at 7:14 AM
developer.nvidia.com/blog/introdu...
Will this finally be a codon optimizer that works? Still haven’t ever used a magic bullet but I do know not only the codons but the whole sequence play a big role
Will this finally be a codon optimizer that works? Still haven’t ever used a magic bullet but I do know not only the codons but the whole sequence play a big role
You might be asking, "What's the point?"
Point 1: This "synthetic fingerprint" hypothesis is still taken seriously. It was cited uncritically in testimony to the US Senate Committee on Homeland Security. Bad science is influencing policy.
Point 1: This "synthetic fingerprint" hypothesis is still taken seriously. It was cited uncritically in testimony to the US Senate Committee on Homeland Security. Bad science is influencing policy.
October 29, 2025 at 7:32 AM
You might be asking, "What's the point?"
Point 1: This "synthetic fingerprint" hypothesis is still taken seriously. It was cited uncritically in testimony to the US Senate Committee on Homeland Security. Bad science is influencing policy.
Point 1: This "synthetic fingerprint" hypothesis is still taken seriously. It was cited uncritically in testimony to the US Senate Committee on Homeland Security. Bad science is influencing policy.
The genetic code is full of synonymous codons that, for decades, were assumed to be interchangeable.
Today, with NVIDIA, co-led by @genophoria.bsky.social, we announce CodonFM, a family of open-source AI models that reveal the grammar underlying codon choice: developer.nvidia.com/blog/introdu...
Today, with NVIDIA, co-led by @genophoria.bsky.social, we announce CodonFM, a family of open-source AI models that reveal the grammar underlying codon choice: developer.nvidia.com/blog/introdu...
Introducing the CodonFM Open Model for RNA Design and Analysis | NVIDIA Technical Blog
Open research is critical for driving innovation, and many breakthroughs in AI and science are achieved through open collaboration. In the field of digital biology research, NVIDIA Clara supports this...
developer.nvidia.com
October 28, 2025 at 8:55 PM
The genetic code is full of synonymous codons that, for decades, were assumed to be interchangeable.
Today, with NVIDIA, co-led by @genophoria.bsky.social, we announce CodonFM, a family of open-source AI models that reveal the grammar underlying codon choice: developer.nvidia.com/blog/introdu...
Today, with NVIDIA, co-led by @genophoria.bsky.social, we announce CodonFM, a family of open-source AI models that reveal the grammar underlying codon choice: developer.nvidia.com/blog/introdu...
Nuevo Fox y Codón sobre un concepto complicado de explicar. Y por eso lo explicamos. www.youtube.com/watch?v=EfZo...
El "cortismo", un mal del cine actual
YouTube video by TiempoDeCulto Video
www.youtube.com
October 27, 2025 at 1:36 PM
Nuevo Fox y Codón sobre un concepto complicado de explicar. Y por eso lo explicamos. www.youtube.com/watch?v=EfZo...
By modeling codon usage directly, CodonFM achieves multi-fold improvements over prior approaches, revealing how synonymous variation influences expression, variant impact, and therapeutic design.
Learn more in the preprint: research.nvidia.com/labs/dbr/ass...
Learn more in the preprint: research.nvidia.com/labs/dbr/ass...
October 28, 2025 at 8:55 PM
By modeling codon usage directly, CodonFM achieves multi-fold improvements over prior approaches, revealing how synonymous variation influences expression, variant impact, and therapeutic design.
Learn more in the preprint: research.nvidia.com/labs/dbr/ass...
Learn more in the preprint: research.nvidia.com/labs/dbr/ass...
Escherichia coli with a 57-codon genetic code | Science www.science.org/doi/10.1126/...
Escherichia coli with a 57-codon genetic code
The near-universal genetic code uses 64 codons to encode the 20 canonical amino acids and protein synthesis. Here, we designed and generated Escherichia coli with a 4-megabase synthetic genome in whic...
www.science.org
October 26, 2025 at 1:18 AM
Escherichia coli with a 57-codon genetic code | Science www.science.org/doi/10.1126/...
Mesquite 4.02 update released! It fixes a few bugs and adds Codon Alignment and various other improvements. Also, much faster with genomics files with 1000s of loci. www.mesquiteproject.org 🧪 #evolbio
@bembidion.bsky.social
@bembidion.bsky.social
October 25, 2025 at 12:37 AM
Mesquite 4.02 update released! It fixes a few bugs and adds Codon Alignment and various other improvements. Also, much faster with genomics files with 1000s of loci. www.mesquiteproject.org 🧪 #evolbio
@bembidion.bsky.social
@bembidion.bsky.social
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
Announcing our new protein design server evedesign.bio:
• End-to-end protein design for everyone!
• Analyze your generated library interactively and on 3D structures
• Export codon-optimized DNA sequences for experimental testing.
• End-to-end protein design for everyone!
• Analyze your generated library interactively and on 3D structures
• Export codon-optimized DNA sequences for experimental testing.
October 22, 2025 at 2:17 PM
Announcing our new protein design server evedesign.bio:
• End-to-end protein design for everyone!
• Analyze your generated library interactively and on 3D structures
• Export codon-optimized DNA sequences for experimental testing.
• End-to-end protein design for everyone!
• Analyze your generated library interactively and on 3D structures
• Export codon-optimized DNA sequences for experimental testing.
Latest in #GENETICS: Check out a new #rstats package, Codon Usage Bias Analysis (cubar), that can calculate common codon usage indexes in a fast, efficient, and user-friendly manner. buff.ly/7cQcNFn
October 14, 2025 at 8:03 PM
Latest in #GENETICS: Check out a new #rstats package, Codon Usage Bias Analysis (cubar), that can calculate common codon usage indexes in a fast, efficient, and user-friendly manner. buff.ly/7cQcNFn
Get right on that codon optimization for your intron 😉
October 14, 2025 at 12:16 AM
Get right on that codon optimization for your intron 😉
New preprint alert! 🦟 <-> 🦠 <-> 🧑
I am thrilled to share our latest study on alphavirus host adaptation. More specifically, on how a single codon helps blunt alphavirus-induced host innate immune responses in mosquito and human cells. Continue reading for more!
www.biorxiv.org/content/10.1...
I am thrilled to share our latest study on alphavirus host adaptation. More specifically, on how a single codon helps blunt alphavirus-induced host innate immune responses in mosquito and human cells. Continue reading for more!
www.biorxiv.org/content/10.1...
The Sindbis virus nsP3 opal codon protects viral RNA and fitness by maintaining replication spherule integrity
Most alphaviruses encode an in-frame opal stop codon between nsP3 and nsP4 in their nsP ORF. This opal stop codon mediates a temperature-dependent balance between viral polymerase production and prote...
www.biorxiv.org
September 29, 2025 at 11:23 AM
New preprint alert! 🦟 <-> 🦠 <-> 🧑
I am thrilled to share our latest study on alphavirus host adaptation. More specifically, on how a single codon helps blunt alphavirus-induced host innate immune responses in mosquito and human cells. Continue reading for more!
www.biorxiv.org/content/10.1...
I am thrilled to share our latest study on alphavirus host adaptation. More specifically, on how a single codon helps blunt alphavirus-induced host innate immune responses in mosquito and human cells. Continue reading for more!
www.biorxiv.org/content/10.1...
*Ahem*: plant molecular farmer here…just about everything we express in plants is human codon-optimised, and preferably up to 60% G+C - because it just WORKS! So a human-optimised OpenCrispr should be fine in N benth!!
September 27, 2025 at 7:15 PM
*Ahem*: plant molecular farmer here…just about everything we express in plants is human codon-optimised, and preferably up to 60% G+C - because it just WORKS! So a human-optimised OpenCrispr should be fine in N benth!!
Asking the synthetic biology newbies out there to PLEASE check any codon optimizer slop a tool outputs for long homopolymers before ordering synthesis. Lysine comes in two flavors: AAA and AAG. Just because one is more frequent doesn't mean you should have 40 A's in a row in a CDS...
Please check.
Please check.
September 22, 2025 at 2:54 PM
Asking the synthetic biology newbies out there to PLEASE check any codon optimizer slop a tool outputs for long homopolymers before ordering synthesis. Lysine comes in two flavors: AAA and AAG. Just because one is more frequent doesn't mean you should have 40 A's in a row in a CDS...
Please check.
Please check.
Some well-known anti-vaxers are making claims that the ribosome slip/frameshift causes a stop codon to be missed and an own mitochondrial protein to be made, risking autoimmunity.
It´s important to know that the mRNA in COVID-19 vaccines do not contain other protein codes.
(X 6/12/2023)
1/4
It´s important to know that the mRNA in COVID-19 vaccines do not contain other protein codes.
(X 6/12/2023)
1/4
September 20, 2025 at 4:45 PM
Some well-known anti-vaxers are making claims that the ribosome slip/frameshift causes a stop codon to be missed and an own mitochondrial protein to be made, risking autoimmunity.
It´s important to know that the mRNA in COVID-19 vaccines do not contain other protein codes.
(X 6/12/2023)
1/4
It´s important to know that the mRNA in COVID-19 vaccines do not contain other protein codes.
(X 6/12/2023)
1/4
The flexibility of pseudouridine (Ψ) in base pairing remains unclear. Artificial box H/ACA guide RNAs are engineered for targeted pseudouridinylation which reveals the formation of a high-affinity and functional Ψ–Ψ codon-anticodon pair
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A Ψ–Ψ codon–anticodon pairing in nonsense suppression and translational recoding - Nature Chemical Biology
Designer box H/ACA RNA-guided pseudouridylation can target both mRNA and tRNA. Modifying the first U of a stop codon and U36 of the matching anticodon forms one Ψ–Ψ and two Watson–Crick pairs, enablin...
www.nature.com
September 15, 2025 at 7:53 PM
The flexibility of pseudouridine (Ψ) in base pairing remains unclear. Artificial box H/ACA guide RNAs are engineered for targeted pseudouridinylation which reveals the formation of a high-affinity and functional Ψ–Ψ codon-anticodon pair
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The mechanical code of DNA links DNA bending nucleosome organization and codon choice https://www.biorxiv.org/content/10.1101/2025.09.09.675246v1
September 13, 2025 at 5:48 AM
The mechanical code of DNA links DNA bending nucleosome organization and codon choice https://www.biorxiv.org/content/10.1101/2025.09.09.675246v1
A conserved opal termination codon optimizes a temperature-dependent tradeoff between protein production and processing in alphaviruses https://www.biorxiv.org/content/10.1101/2024.08.21.609082v1
A conserved opal termination codon optimizes a temperature-dependent tradeoff between protein production and processing in alphaviruses https://www.biorxiv.org/content/10.1101/2024.08.21.609082v1
Alphaviruses are enveloped, single-stranded, positive-sense RNA viruses that often require transmiss
www.biorxiv.org
August 22, 2024 at 9:17 PM
A conserved opal termination codon optimizes a temperature-dependent tradeoff between protein production and processing in alphaviruses https://www.biorxiv.org/content/10.1101/2024.08.21.609082v1
8) Das Ribosom fährt vereinfacht gesagt die mRNA entlang und übersetzt die Triplets in Aminosäuren.
Wer will, kann an dieser Stelle selbst Ribosom spielen und versuchen, unsere Sequenz mithilfe der „Code-Sonne“ von Wikipedia zu übersetzen:
AGC UGC AUU GAA AAC UGC GAA
Wer will, kann an dieser Stelle selbst Ribosom spielen und versuchen, unsere Sequenz mithilfe der „Code-Sonne“ von Wikipedia zu übersetzen:
AGC UGC AUU GAA AAC UGC GAA
January 5, 2024 at 4:57 PM
8) Das Ribosom fährt vereinfacht gesagt die mRNA entlang und übersetzt die Triplets in Aminosäuren.
Wer will, kann an dieser Stelle selbst Ribosom spielen und versuchen, unsere Sequenz mithilfe der „Code-Sonne“ von Wikipedia zu übersetzen:
AGC UGC AUU GAA AAC UGC GAA
Wer will, kann an dieser Stelle selbst Ribosom spielen und versuchen, unsere Sequenz mithilfe der „Code-Sonne“ von Wikipedia zu übersetzen:
AGC UGC AUU GAA AAC UGC GAA
This is just because ! worked with R. sphaeroides during my PhD and I was quite familiar with the system. The cas9 sequence we used is codon harmonized to the GC content of R. sphaeroides (69%) which is quite similar to the one of C. necator (66%). So, we thought to give it a try!
November 25, 2024 at 4:42 PM
This is just because ! worked with R. sphaeroides during my PhD and I was quite familiar with the system. The cas9 sequence we used is codon harmonized to the GC content of R. sphaeroides (69%) which is quite similar to the one of C. necator (66%). So, we thought to give it a try!