Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social (@RolandDunbrack) / X

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social

12.3K posts

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social

@RolandDunbrack

Comp struct bio. Gay&proud 🏳️‍🌈. Views my own & not my employer's.

Philadelphia and Provincetown

Joined June 2012

Pinned
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
Jun 20, 2024
Here's my talk at the 1st 🏳️‍🌈LGBTQI+ @iscb Symposium, which was held on Monday online. It's about how coming out intersected with my education and scientific career. It's quite personal so if that's not your thing, skip it. Other talks on the ISCB channel.
24K
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
May 8, 2024
Demis -- I think AlphaFold3 is really exciting. As Reviewer #3, I got great results from the server. I tried hard to get @Nature to urge you to release the code but was unsuccessful. I did not get it for re-review so I don't know if you responded. So why no code? @GoogleDeepMind
Demis Hassabis
@demishassabis
May 8, 2024
Thrilled to announce AlphaFold 3 which can predict the structures and interactions of nearly all of life’s molecules with state-of-the-art accuracy including proteins, DNA and RNA. Biology is a complex dynamical system so modeling interactions is crucial blog.google/technology/ai/…
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
May 10, 2024
But no one besides Novartis& Lilly etc. has access to the ligand structure prediction. All the data on ligand binding in the paper is irreproducible and should not have been published. As Reviewer #3 for @Nature I recommended taking it out and saving it for promotional material.
Isomorphic Labs
@IsomorphicLabs
May 8, 2024
We're excited to announce #AlphaFold 3 with @GoogleDeepMind in @Nature: our new AI model for predicting biomolecule structures with unprecedented breadth and accuracy. Expanding beyond proteins to tackle DNA, RNA, small molecules to fuel advances in biology & drug design 🧵
00:00
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
Oct 15, 2024
Replying to @matthewremski
I bet the @nytimes reports this with a headline “Trump enjoys music with his followers.”
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
May 8, 2024
Replying to @pedrobeltrao
As a reviewer #3 of the paper, I tried REALLY HARD to get @Nature to demand downloadable code. The editors just ghosted me. I wrote extensively that the server needed work but I was not given the paper to re-review so I don't know if they improved it. It's not available yet.
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
Feb 23, 2023
Wow, #AlphaFold 2.3 is producing great results on protein complexes that did not work in 2.1 or 2.2. Previously we would get proteins or peptides not bound at all, or poor iPTM scores & inconsistent results from models 1-5. Now on several systems we get results that make sense.
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
May 13, 2024
There is no such thing as AlphaFold3. There is only alphafoldserver.com. The difference is throttling rigorous scientific and biomedical research.
54K
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
May 8, 2024
Replying to @RolandDunbrack
In my review, I made a list of much science that happened bc AlphaFold2 code was released. I suggested that so much science will not happen if AlphaFold3 code is not released (or not with AF3 itself). We've made ~100k models with AF2 code. How could we use a server for all that?
78K
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
Jul 24, 2023
I just refused to review an article for the journal Structure with this message.
30K
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
Jun 24, 2024
Alphafold3 models of BRCA1 interacting with PALB2. That's a lot of hallucination. The models are ~90% hallucinated alpha helices.
46K
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
May 24, 2024
So I was chatting with somebody who was showing me some structures, and he typed "set grid_mode,1" in pymol and it shows all the active objects in a grid, and they all rotate and move at the same time with the mouse. I was like, "I didn't know it could do that..."
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Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
Jul 1, 2023
Kurt Wüthrich thinks he is discriminated against because he is a man at the #lino23 meeting because he had to listen to concerns about diversity in science. You can't make this shit up. I wonder if he realizes how clueless he is. Listen at 28:55 and 46:35.
The Future of Structural Biology - Agora Talks | Lindau Mediatheque
From mediatheque.lindau-nobel.org
157K
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
Dec 21, 2020
We created a website & Python script that renumbers residues in PDB files with UniProt numbering. It returns mmCIF & PDB format files of the ASU & bio assemblies for any list of entries or UniProtIDs. Plz help us test it. @buildmodels @PDBj_en @PDBeurope dunbrack3.fccc.edu/PDBrenum/
Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social
@RolandDunbrack
Jul 7, 2021
Our short paper on "PDBrenum: A webserver and program providing PDB renumbered according to their UniProt sequences" is now available. journals.plos.org/plosone/articl… Webserver is at dunbrack3.fccc.edu/PDBrenum. Download mmCIF/PDB & ASU/Bioassembly files.@buildmodels @PDBeurope @PDBj_en
journals.plos.org
PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their...
The Protein Data Bank (PDB) was established at Brookhaven National Laboratories in 1971 as an archive for biological macromolecular crystal structures. In mid 2021, the database has almost 180,000...