Jameel Abduljalil
@jameel-abduljalil.bsky.social
PhD candidate in (Computational) Structural Biology at the University of Sydney.
Personal account.
Personal account.
Can anyone @mscommunity.bsky.social tell me how to stop Microsoft from controlling my laptop files? Don’t tell me it’s “for my own good”—it’s not. Their awful sync feature just wiped out ~30 hours of work. I don’t want their cloud storage. I don’t want them snooping in my desktop files.
August 16, 2025 at 2:00 AM
Can anyone @mscommunity.bsky.social tell me how to stop Microsoft from controlling my laptop files? Don’t tell me it’s “for my own good”—it’s not. Their awful sync feature just wiped out ~30 hours of work. I don’t want their cloud storage. I don’t want them snooping in my desktop files.
Reposted by Jameel Abduljalil
🧬🧫🦠 @science.org Bacterial reverse transcriptase synthesizes long poly-A–rich cDNA for antiphage defense | Science www.science.org/doi/10.1126/... #microbiology #bacteriophage #antiphage #immunity #DNA #RNAsky #RT #Cryo-EM #DRT9
May 2, 2025 at 9:02 PM
🧬🧫🦠 @science.org Bacterial reverse transcriptase synthesizes long poly-A–rich cDNA for antiphage defense | Science www.science.org/doi/10.1126/... #microbiology #bacteriophage #antiphage #immunity #DNA #RNAsky #RT #Cryo-EM #DRT9
Reposted by Jameel Abduljalil
Okay class, today we're going to discuss damped harmonic oscillation.
April 7, 2025 at 4:22 PM
Okay class, today we're going to discuss damped harmonic oscillation.
Reposted by Jameel Abduljalil
🚀 #AlphaFold Database update
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
March 3, 2025 at 4:33 PM
🚀 #AlphaFold Database update
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
AlphaFold DB now integrates The Encyclopedia of Domains (TED) – a resource designed to systematically identify & classify structural domains within AlphaFold-predicted protein structures.
www.ebi.ac.uk/about/news/u...
@pdbeurope.bsky.social
Reposted by Jameel Abduljalil
Early signs of deception, cheating & self-preservation in top-performing models in terms of reasoning are extremely worrisome. We don't know how to guarantee AI won't have undesired behavior to reach goals & this must be addressed before deploying powerful autonomous agents.
time.com/7259395/ai-c...
time.com/7259395/ai-c...
When AI Thinks It Will Lose, It Sometimes Cheats
When sensing defeat in a match against a skilled chess bot, advanced models sometimes hack their opponent, a study found.
time.com
February 20, 2025 at 4:45 PM
Early signs of deception, cheating & self-preservation in top-performing models in terms of reasoning are extremely worrisome. We don't know how to guarantee AI won't have undesired behavior to reach goals & this must be addressed before deploying powerful autonomous agents.
time.com/7259395/ai-c...
time.com/7259395/ai-c...
Folks, Gandalf is right. I wish I had known that advice before.
February 18, 2025 at 7:48 PM
Folks, Gandalf is right. I wish I had known that advice before.
Even scaffold-based splitting didn't work for Frodo!
February 11, 2025 at 3:16 AM
Even scaffold-based splitting didn't work for Frodo!
Trying to access the MacKerell lab website is a bloody frustrating experience. @umbaltimore.bsky.social, please it's 2025 and we still face this saga! For the past three years, I was lucky three or four times to reach the page.
February 9, 2025 at 9:46 AM
Trying to access the MacKerell lab website is a bloody frustrating experience. @umbaltimore.bsky.social, please it's 2025 and we still face this saga! For the past three years, I was lucky three or four times to reach the page.
Reposted by Jameel Abduljalil
Very nice to see the work of Matt Warren and Isak Valsson just out with Charlotte Deane, Aniket Magarkar and @garrettmm.bsky.social where we show how augementation can dramatically improve ML affinity predictions to close to FEP accuracy.
rdcu.be/d88Wm
rdcu.be/d88Wm
Narrowing the gap between machine learning scoring functions and free energy perturbation using augmented data
Communications Chemistry - Machine learning offers great promise for fast and accurate binding affinity predictions, however, current models lack robust evaluation and fail on tasks encountered in...
rdcu.be
February 8, 2025 at 8:12 PM
Very nice to see the work of Matt Warren and Isak Valsson just out with Charlotte Deane, Aniket Magarkar and @garrettmm.bsky.social where we show how augementation can dramatically improve ML affinity predictions to close to FEP accuracy.
rdcu.be/d88Wm
rdcu.be/d88Wm
A PhD student teaching an honours student how to create a colorful figure.
February 4, 2025 at 10:22 AM
A PhD student teaching an honours student how to create a colorful figure.
Inspired by the architecture of AlphaFold2
www.nature.com/articles/s41...
www.nature.com/articles/s41...
NuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation - Nature Communications
The 3D structure of RNA is crucial for unraveling its functions. Here, the authors developed NuFold, an end-to-end deep learning-based approach that predicts all-atom RNA 3D structures from sequences....
www.nature.com
January 27, 2025 at 11:39 AM
Inspired by the architecture of AlphaFold2
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Author's Contribution: Meowzart McWhiskers contributed to the project's logistics and assisted in manuscript writing.
January 27, 2025 at 11:21 AM
Author's Contribution: Meowzart McWhiskers contributed to the project's logistics and assisted in manuscript writing.
Reposted by Jameel Abduljalil
We have an exciting opportunity for a new independent group leader with an interest in structural/molecular biology and machine learning to join our Division of Structural Studies at the @mrclmb.bsky.social! 🥳
Re-posts appreciated.
www.nature.com/naturecareer...
Re-posts appreciated.
www.nature.com/naturecareer...
Research Group Leader Tenure Track - Structural Studies - LMB 2549 - Cambridgeshire job with MRC Laboratory of Molecular Biology | 12835196
Research Group Leader Tenure Track Starting Salary £65,940 to £74,448 per annum MRC Laboratory of Molecular Biology, Cambridge, UK
www.nature.com
January 27, 2025 at 9:38 AM
We have an exciting opportunity for a new independent group leader with an interest in structural/molecular biology and machine learning to join our Division of Structural Studies at the @mrclmb.bsky.social! 🥳
Re-posts appreciated.
www.nature.com/naturecareer...
Re-posts appreciated.
www.nature.com/naturecareer...
"Back then, we were trained to identify bacteria through the smell of their culture", he added.
January 25, 2025 at 10:20 AM
"Back then, we were trained to identify bacteria through the smell of their culture", he added.
Reposted by Jameel Abduljalil
💡💥Here’s a modest proposal I’ve been pondering for a while on how to change the PEER REVIEW process and start more community-driven SCIENCE FUNDING. Lots of feedback/discussion welcomed! Other variants of the idea might exist already—not claiming originality. (a long 🧵) (1/9)
November 30, 2024 at 5:14 AM
💡💥Here’s a modest proposal I’ve been pondering for a while on how to change the PEER REVIEW process and start more community-driven SCIENCE FUNDING. Lots of feedback/discussion welcomed! Other variants of the idea might exist already—not claiming originality. (a long 🧵) (1/9)
Reposted by Jameel Abduljalil
AlphaFold3 still tends to overfit regions that AF2 multimer predicts to be disordered. Almost all disordered regions become helices in AF3.
December 15, 2024 at 2:03 AM
AlphaFold3 still tends to overfit regions that AF2 multimer predicts to be disordered. Almost all disordered regions become helices in AF3.
Reposted by Jameel Abduljalil
I've created a new plugin for #PyMOL (called PyMOLfold) that allows you to fold protein sequences right in the GUI. Simply select your model of choice (e.g., #ESM3, Boltz-1) and paste in your amino acid sequence.
github.com/colbyford/Py...
#ai #proteinfolding #alphafold
github.com/colbyford/Py...
#ai #proteinfolding #alphafold
December 13, 2024 at 1:46 PM
I've created a new plugin for #PyMOL (called PyMOLfold) that allows you to fold protein sequences right in the GUI. Simply select your model of choice (e.g., #ESM3, Boltz-1) and paste in your amino acid sequence.
github.com/colbyford/Py...
#ai #proteinfolding #alphafold
github.com/colbyford/Py...
#ai #proteinfolding #alphafold
Reposted by Jameel Abduljalil
Crosslinks can sometimes improve AlphaFold3 models. Crosslinking is an experimental method often used as a source of distance restraints in modeling. In AlphaFold3, instead of using restraints, crosslinks can be included as covalent ligands. Thanks to Agnieszka Obarska-Kosinska for the idea.
December 4, 2024 at 9:40 AM
Crosslinks can sometimes improve AlphaFold3 models. Crosslinking is an experimental method often used as a source of distance restraints in modeling. In AlphaFold3, instead of using restraints, crosslinks can be included as covalent ligands. Thanks to Agnieszka Obarska-Kosinska for the idea.
Reposted by Jameel Abduljalil
Exclusive: New hijacking scam targets Elsevier, Springer Nature, and other major publishers
@abalkina.bsky.social has the scoop
@abalkina.bsky.social has the scoop
Exclusive: New hijacking scam targets Elsevier, Springer Nature, and other major publishers
Until recently, journal hijackers do not appear to have targeted titles from big publishers, in part because their well-known website designs made such clones easy to detect. Typically, cloned vers…
retractionwatch.com
November 25, 2024 at 6:37 PM
Exclusive: New hijacking scam targets Elsevier, Springer Nature, and other major publishers
@abalkina.bsky.social has the scoop
@abalkina.bsky.social has the scoop
Reposted by Jameel Abduljalil
Reposted by Jameel Abduljalil
One more Dean joke (from my dad)...
If you are driving and see a carcass by the side of the road, how can you tell if it's a deer or a dean?
If you see skid marks in front of the carcass, it's a deer.
If you are driving and see a carcass by the side of the road, how can you tell if it's a deer or a dean?
If you see skid marks in front of the carcass, it's a deer.
a cartoon monkey wearing a pirate hat is playing drums in a band
ALT: a cartoon monkey wearing a pirate hat is playing drums in a band
media.tenor.com
November 29, 2024 at 6:18 PM
One more Dean joke (from my dad)...
If you are driving and see a carcass by the side of the road, how can you tell if it's a deer or a dean?
If you see skid marks in front of the carcass, it's a deer.
If you are driving and see a carcass by the side of the road, how can you tell if it's a deer or a dean?
If you see skid marks in front of the carcass, it's a deer.