Pinned
Bernardo Pinto
@pintobi.bsky.social
· Oct 25
Happy to share this preprint showing how to use AlphaFold2 conformational sampling techniques pioneered by @ddelalamo.bsky.social to obtain a closed state of Potassium channels. www.biorxiv.org/content/10.1...
Reposted by Bernardo Pinto
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 Bernardo Pinto
You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly.
This saves some clicking around. Neat!
This saves some clicking around. Neat!
October 7, 2025 at 2:54 PM
You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly.
This saves some clicking around. Neat!
This saves some clicking around. Neat!
Reposted by Bernardo Pinto
I get that the news cycle is packed right now, but I just heard from a colleague at the Smithsonian that this is fully a GIANT SQUID BEING EATEN BY A SPERM WHALE and it’s possibly the first ever confirmed video according to a friend at NOAA
10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
September 24, 2025 at 8:30 PM
I get that the news cycle is packed right now, but I just heard from a colleague at the Smithsonian that this is fully a GIANT SQUID BEING EATEN BY A SPERM WHALE and it’s possibly the first ever confirmed video according to a friend at NOAA
10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
10 YEAR OLD ME IS LOSING HER MIND (a thread 🧵)
Reposted by Bernardo Pinto
THE VIDEO IS HERE!!!
You asked for it! We delivered Quack-O-Grams to our members of Congress urging them to #ImpeachRFK, and get that Quack out of office!
There's still time for you to get in on this fluffy, feathery action: Send your own duck at zurl.co/W1ZnB and keep the momentum going! 🦆
There's still time for you to get in on this fluffy, feathery action: Send your own duck at zurl.co/W1ZnB and keep the momentum going! 🦆
September 17, 2025 at 9:36 PM
THE VIDEO IS HERE!!!
Reposted by Bernardo Pinto
He's making a list, he's checkin' it twice
He's gonna find out who's naughty or nice
RW Official Sleuth Whitelist is out!
If you aren't on it, you are trash.
retractionwatch.com/2018/06/17/m...
He's gonna find out who's naughty or nice
RW Official Sleuth Whitelist is out!
If you aren't on it, you are trash.
retractionwatch.com/2018/06/17/m...
Meet the scientific sleuths: More than two dozen who’ve had an impact on the scientific literature
Over the years, we have written about a number of the sleuths who, on their own time and often at great risks to their careers or finances, have looked for issues in the scientific literature. Here…
retractionwatch.com
August 19, 2025 at 1:07 PM
He's making a list, he's checkin' it twice
He's gonna find out who's naughty or nice
RW Official Sleuth Whitelist is out!
If you aren't on it, you are trash.
retractionwatch.com/2018/06/17/m...
He's gonna find out who's naughty or nice
RW Official Sleuth Whitelist is out!
If you aren't on it, you are trash.
retractionwatch.com/2018/06/17/m...
Reposted by Bernardo Pinto
Fantastic new paper by @reeserichardson.bsky.social et al.
An enormous amount of work showing the extent of coordinated scientific fraud and involvement of some editors.
The number of fraudulent publications grows at a rate far outpacing that of legitimate science.
www.pnas.org/doi/10.1073/...
An enormous amount of work showing the extent of coordinated scientific fraud and involvement of some editors.
The number of fraudulent publications grows at a rate far outpacing that of legitimate science.
www.pnas.org/doi/10.1073/...
August 4, 2025 at 9:27 PM
Fantastic new paper by @reeserichardson.bsky.social et al.
An enormous amount of work showing the extent of coordinated scientific fraud and involvement of some editors.
The number of fraudulent publications grows at a rate far outpacing that of legitimate science.
www.pnas.org/doi/10.1073/...
An enormous amount of work showing the extent of coordinated scientific fraud and involvement of some editors.
The number of fraudulent publications grows at a rate far outpacing that of legitimate science.
www.pnas.org/doi/10.1073/...
Reposted by Bernardo Pinto
PSA = Google Colab Pro free for one year for academic use (US only):
blog.google/outreach-ini...
blog.google/outreach-ini...
New Google Colab features for higher education
Google Colab offers free Colab Pro for students, interactive slideshows and AI controls in notebooks.
blog.google
July 22, 2025 at 12:33 AM
PSA = Google Colab Pro free for one year for academic use (US only):
blog.google/outreach-ini...
blog.google/outreach-ini...
Reposted by Bernardo Pinto
Reposted by Bernardo Pinto
Zero-shot antibody design in a 24-well plate [new]
Achieves high hit rates for de novo antibody/nanobody and miniprotein design, validated experimentally against diverse targets without prior binders.
Achieves high hit rates for de novo antibody/nanobody and miniprotein design, validated experimentally against diverse targets without prior binders.
July 7, 2025 at 4:27 AM
Zero-shot antibody design in a 24-well plate [new]
Achieves high hit rates for de novo antibody/nanobody and miniprotein design, validated experimentally against diverse targets without prior binders.
Achieves high hit rates for de novo antibody/nanobody and miniprotein design, validated experimentally against diverse targets without prior binders.
Reposted by Bernardo Pinto
Predicted structures from the AFDB are poor substitutes for experimental structures when training inverse folding NNs. Here, authors show that this is because they are "too perfect", and passing them through a custom-trained AFDB-to-PDB NN helps fix this
threadreaderapp.com/thread/19384...
threadreaderapp.com/thread/19384...
June 27, 2025 at 11:33 AM
Predicted structures from the AFDB are poor substitutes for experimental structures when training inverse folding NNs. Here, authors show that this is because they are "too perfect", and passing them through a custom-trained AFDB-to-PDB NN helps fix this
threadreaderapp.com/thread/19384...
threadreaderapp.com/thread/19384...
Reposted by Bernardo Pinto
I listened to the @rorinstitute.bsky.social talk about Funding by Algorithm bsky.app/profile/rori...
I think it's arrogant and dangerous to suppose that AI has a role in assessing grants. @astrokatie.com says why, very clearly.
I think it's arrogant and dangerous to suppose that AI has a role in assessing grants. @astrokatie.com says why, very clearly.
Chatbots — LLMs — do not know facts and are not designed to be able to accurately answer factual questions. They are designed to find and mimic patterns of words, probabilistically. When they’re “right” it’s because correct things are often written down, so those patterns are frequent. That’s all.
June 20, 2025 at 10:02 PM
I listened to the @rorinstitute.bsky.social talk about Funding by Algorithm bsky.app/profile/rori...
I think it's arrogant and dangerous to suppose that AI has a role in assessing grants. @astrokatie.com says why, very clearly.
I think it's arrogant and dangerous to suppose that AI has a role in assessing grants. @astrokatie.com says why, very clearly.
Reposted by Bernardo Pinto
NEW: A federal judge has ruled that the Trump administration’s termination of hundreds of NIH grants was “void and illegal.”
He ordered funding for some of the grants, including many profiled by ProPublica in recent months, to be reinstated.
By @anniewaldman.bsky.social
He ordered funding for some of the grants, including many profiled by ProPublica in recent months, to be reinstated.
By @anniewaldman.bsky.social
Federal Judge Deems Trump Administration’s Termination of NIH Grants Illegal
In a ruling issued Monday, the judge called the government’s directives “arbitrary and capricious” and ordered funding for some of the NIH grants, including many profiled by ProPublica in recent month...
www.propublica.org
June 17, 2025 at 3:17 PM
NEW: A federal judge has ruled that the Trump administration’s termination of hundreds of NIH grants was “void and illegal.”
He ordered funding for some of the grants, including many profiled by ProPublica in recent months, to be reinstated.
By @anniewaldman.bsky.social
He ordered funding for some of the grants, including many profiled by ProPublica in recent months, to be reinstated.
By @anniewaldman.bsky.social
Reposted by Bernardo Pinto
“The search is on for 25 researchers from around the world in Lund University’s largest ever international recruitment drive. The main focus will be on AI research and other areas in which the University has a strategic focus.”
www.lunduniversity.lu.se/article/lund...
www.lunduniversity.lu.se/article/lund...
Lund University launches largest-ever global recruitment drive for researchers
Lund University. Lund University’s body of researchers is getting reinforcements. If all goes according to plan, no fewer than 25 new researchers from all over the world will arrive in Lund this autum...
www.lunduniversity.lu.se
June 12, 2025 at 7:07 PM
“The search is on for 25 researchers from around the world in Lund University’s largest ever international recruitment drive. The main focus will be on AI research and other areas in which the University has a strategic focus.”
www.lunduniversity.lu.se/article/lund...
www.lunduniversity.lu.se/article/lund...
Reposted by Bernardo Pinto
Thanks Ian for your leadership and great meeting you today at NIH!
I'm overwhelmed by the outpouring of support and kind words from people within and outside NIH to us. Many people at the NIH have reached out to ask me if they can still sign on to the #BethesdaDeclaration. *Yes*, NIH employees can still sign at this link. The list of signatories will be updated!
Bethesda Declaration — STAND UP FOR SCIENCE
Support NIH Staff Now!
www.standupforscience.net
June 12, 2025 at 1:39 AM
Thanks Ian for your leadership and great meeting you today at NIH!
Reposted by Bernardo Pinto
PSA: If you're trying to run the Boltz ColabFold notebook and finding that it's crashing with this error, it's because you need to switch to an A100 GPU; the notebook no longer works with T4/L4 GPUs
June 8, 2025 at 9:14 AM
PSA: If you're trying to run the Boltz ColabFold notebook and finding that it's crashing with this error, it's because you need to switch to an A100 GPU; the notebook no longer works with T4/L4 GPUs
Reposted by Bernardo Pinto
A case study on the challenges of evaluating AI predictions in biology and the implications for published results.
1/2
rachel.fast.ai/posts/2025-0...
1/2
rachel.fast.ai/posts/2025-0...
Rachel Thomas, PhD - Deep learning gets the glory, deep fact checking gets ignored
an AI researcher going back to school for immunology
rachel.fast.ai
June 5, 2025 at 12:41 AM
A case study on the challenges of evaluating AI predictions in biology and the implications for published results.
1/2
rachel.fast.ai/posts/2025-0...
1/2
rachel.fast.ai/posts/2025-0...
Reposted by Bernardo Pinto
Our work on deriving protein-protein (functional) associations across different human tissues from proteomics data is now published. There is quite a lot in this paper, so I will just touch on a few highlights:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A tissue-specific atlas of protein–protein associations enables prioritization of candidate disease genes - Nature Biotechnology
Protein–protein interactions specific to 11 individual tissues are presented in a comprehensive resource.
www.nature.com
May 2, 2025 at 10:31 AM
Our work on deriving protein-protein (functional) associations across different human tissues from proteomics data is now published. There is quite a lot in this paper, so I will just touch on a few highlights:
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Bernardo Pinto
Reposted by Bernardo Pinto
I am shocked by the news coming from the NIH. I was a postdoc there and know many of the PIs affected at NINDS. Don’t be naive, this is a deliberate attack meant to cripple the system. No scientist is safe, regardless of political stance or whether you have remained neutral
April 1, 2025 at 5:01 PM
I am shocked by the news coming from the NIH. I was a postdoc there and know many of the PIs affected at NINDS. Don’t be naive, this is a deliberate attack meant to cripple the system. No scientist is safe, regardless of political stance or whether you have remained neutral
Reposted by Bernardo Pinto
THREAD
The numbers are in. @bsky.app research sharing volumes vs X Formerly Twitter
In March 2024, on most days, Bluesky hosts more posts linked to research published in 2025 than X.
By quite a lot.
Release the Kraken...
#AcademicSky #HigherEd #Altmetrics
1/11
The numbers are in. @bsky.app research sharing volumes vs X Formerly Twitter
In March 2024, on most days, Bluesky hosts more posts linked to research published in 2025 than X.
By quite a lot.
Release the Kraken...
#AcademicSky #HigherEd #Altmetrics
1/11
March 27, 2025 at 5:22 PM
THREAD
The numbers are in. @bsky.app research sharing volumes vs X Formerly Twitter
In March 2024, on most days, Bluesky hosts more posts linked to research published in 2025 than X.
By quite a lot.
Release the Kraken...
#AcademicSky #HigherEd #Altmetrics
1/11
The numbers are in. @bsky.app research sharing volumes vs X Formerly Twitter
In March 2024, on most days, Bluesky hosts more posts linked to research published in 2025 than X.
By quite a lot.
Release the Kraken...
#AcademicSky #HigherEd #Altmetrics
1/11
Reposted by Bernardo Pinto
Roses are red
Violets are blue
Violets are blue
March 20, 2025 at 5:43 PM
Roses are red
Violets are blue
Violets are blue
Reposted by Bernardo Pinto
FREEDOM OF EXPRESSION FOR HETEROCHROMATIN
Lucky to stay ahead of today’s NIH that would cancel language implying that heterochromatin isn’t the good chromatin.
March 20, 2025 at 7:00 PM
FREEDOM OF EXPRESSION FOR HETEROCHROMATIN
Reposted by Bernardo Pinto
Reposted by Bernardo Pinto
