Daniel Rigden

OK, so I'm not deleting this account (yet) but I am switching to the friendlier alternative. See you over there.

BIG MISTAKE BY DOZY DON!!!!! SPACE COMMAND BELONGS IN SAN FRANCISCO, NOT ALABAMA (A TOTAL DISASTER OF A STATE). EVERYONE KNOWS SAN FRANCISCO IS THE FUTURE HOME OF "STAR FLEET ACADEMY" ("LIVE LONG AND PROSPER"). THAT’S BECAUSE CALIFORNIA IS #1 FOR AEROSPACE, #1 FOR TECHNOLOGY, #1 FOR AI (ARTIFICIAL INTELLIGENCE, VERY SMART PEOPLE, MUCH SMARTER THAN JD “JUST DANCE” VANCE, WHO HAS LOW IQ). SAN FRANCISCO IS THE BEST IN THE WORLD FOR ENGINEERING AND INNOVATION... ROCKETS, SOFTWARE, "THE STARTUPS.” ALABAMA’S GOVERNOR “KRAZY” KAY HAS NO IDEA WHAT IS GOING ON. JUST LIKE LITTLE HANDS, SHE IS SLOW AND BURPS A LOT. SHE HAS DONE NOTHING FOR HER PEOPLE AND MADE THE STATE VERY UNSAFE!!! A MURDER RATE 190% HIGHER THAN CALIFORNIA’S. "SPACE COMMAND" MUST BE HERE IN CALIFORNIA, THE GREATEST STATE IN AMERICA, WITH ME, THE YOUNG AND BEAUTIFUL GOVERNOR GAVIN C. NEWSOM. THE SLEEPY GOLFER IN THE WHITE HOUSE DIDN’T MOVE IT HERE. HE HAS NEWSOM DERANGEMENT SYNDROME (NDS). SAD!!! — GCN

CASP is getting cut by NIH... 😢 (Anyone with extra funds wanna help support perhaps the most important competition of the century?) science.org/content/articl…

ABCFold: Easier Running and Comparison of AlphaFold 3, Boltz-1, and Chai-1 - Structural biology has seen a revolution with deep learning-based protein structure predictors like AlphaFold 3, Boltz-1, and Chai-1. However, running and comparing these models efficiently remains a challenge. - ABCFold is a new tool that simplifies the process of running and benchmarking AlphaFold 3, Boltz-1, and Chai-1, allowing users to generate structure predictions with a standardized input format. - The tool converts AlphaFold 3 JSON inputs into compatible formats for Boltz-1 and Chai-1, enabling seamless execution of all three models from a single input. - ABCFold provides automated multiple sequence alignment (MSA) handling, supporting both JackHMMER-based searches and the MMseqs2 API. Users can also supply custom MSAs and template structures. - The software includes a unified output visualization framework, allowing side-by-side comparison of model predictions, pLDDT scores, and predicted aligned error (PAE) values. Structural clashes are also highlighted for better assessment. - One of the key benefits of ABCFold is its ability to automate installation and version management of Boltz-1 and Chai-1, reducing setup complexity for researchers. - By providing standardized evaluation metrics and interactive visualization tools, ABCFold enhances reproducibility and helps researchers assess the relative strengths of different structure prediction methods. - This tool is an important step toward better benchmarking of next-generation protein structure predictors, enabling broader adoption and more effective model selection for specific biological applications. @DanielRigden 💻Code: github.com/rigdenlab/ABCF… 📜Paper: biorxiv.org/content/10.110… #StructuralBiology #AlphaFold #MachineLearning #ProteinFolding #DeepLearning #Bioinformatics #ComputationalBiology

@LivUniISMIB findaphd.com/phds/project/b…

🚨 New PhD Opening ! 🚨 Leveraging Deep Learning-based bioinformatics for experimental structural biology Interested in working where structural bioinformatics meets X-ray crystallography? If so, this *fully-funded* PhD project could be for you! @LivUniISMIB Link in reply

How many of the PDB models that were solved using experimental phasing could have been solved by molecular replacement using models obtained from AlphaFold? @ActaCrystD @IUCr #MolecularReplacement #AlphaFold2 #ComputationalMethods doi.org/10.1107/S20597…

This was a mistake. It would have been a powerful statement having somebody there representing the Axis forces.

@gjbarton @UoDLifeSciences @dundeewestend @DDWaterfront Fabulous. I loving watching (and hearing) them go by

Geese over #dundee #scotland at dusk today. Best with sound on! ⁦@UoDLifeSciences⁩ ⁦@dundeewestend⁩ ⁦@DDWaterfront⁩

If ever we needed a laugh it was now, so I am giving away three free copies of my new paperback - signed and dedicated to you or anyone of your choosing. Makes an excellent cheapskate Christmas present. Just retweet this message and I will pick three at random...

@hrobinsonmuseum Delightful!

The other side of William Heath Robinson. Date 1935 Medium - cut paper collage Dimensions Width 236mm Height 284mm Let us know what you think about this rare William Heath Robinson piece. #williamheathrobinson #heathrobinson #pinner #theothersideofwilliamheathrobinson

I've never received so many prayers from atheists.

AlphaFold 2, but not AlphaFold 3, Predicts Confident but Unrealistic Beta-Solenoid Structures for Repeat Proteins • This study investigates AlphaFold 2’s (AF2) tendency to predict high-confidence yet biologically implausible β-solenoid structures for artificial repeat sequences, a potential blind spot in AF2. • When given random sequences with perfect repeats, AF2 often predicts β-solenoids with high pLDDT scores, despite unusual features such as stacked, uncompensated charged residues, which are energetically unfavorable. • Molecular Dynamics simulations reveal instability in these AF2-predicted structures, contrasting with the stable behavior of experimentally validated β-solenoids. • Comparative modeling with AlphaFold 3, ESMFold, and RoseTTAFold shows that these models frequently predict disordered or alternate structures for the same sequences, suggesting that AF2’s issue is unique. • The study suggests this bias may affect predictions for natural repeat proteins, indicating a need for caution when interpreting AF2 results for certain classes of repetitive proteins. • Results emphasize the importance of using multiple prediction models and validation methods when interpreting structures for repeat-rich proteins. @DanielRigden @AJSimpkin 📜Paper: biorxiv.org/content/10.110… #AlphaFold #ProteinStructure #Bioinformatics #BetaSolenoid #StructuralBiology #DeepLearning

Thanks to this valuable account for a useful and speedy (<3 h!) summary of our latest work, a team effort led by talented MSc student Olivia Pratt

Coming soon to a town near you, while our leaders serve billionaire psychopaths & the media distracts us with inanity & bile.

Poorest households gain most, wealthiest pay most in the Budget - Treasury impact assessment.

@rborza_ @simonduerr @NIAIDNews @NAR_Open It sounds like a user needs to apply for a license to publish a high-quality figure. Their response says that will be free, as I say

@DanielRigden @simonduerr @NIAIDNews @NAR_Open So, is it correct that a publication license is planned for release? And it will be free of charge? Do you have any details on when this is expected to happen?

🚨 Great alternatives to BioRender are now available!! 📢 @NIAIDNews offers a collection of public figures and icons for everyone to use. Check it out at bioart.niaid.nih.gov

@simonduerr @rborza_ @NIAIDNews @NAR_Open ... provided that users properly cite the relevant GDP publications and website according to our citation guidelines." It seems reasonable that they want credit for their efforts, but users will vote with their feet if the procedure is too burdensome [2/2]

@simonduerr @rborza_ @NIAIDNews @NAR_Open The reviewers and I queried these issues. Quoting part of the response "non-public educational uses and low-resolution image downloads will remain free of charge. For high-quality, publication-level usage, we will grant a publication license at no cost ... [1/2]

@hariharan_algia @rborza_ @NIAIDNews @NAR_Open Yes

@DanielRigden @rborza_ @NIAIDNews @NAR_Open @DanielRigden is biogdp free ?