Hmm, the CCD code option disappeared from the #AlphaFold3 server...
22.01.2025 00:06 — 👍 1 🔁 0 💬 0 📌 0
An update to #AlphaFold3 server. Now, you can add any ligand from the PDB using a CCD Code (up to 2024_10_28). Here is an MPro #SARS-CoV2 inhibitor from PDB 8u9h. The crystal structure is grey, and the #AF3 model is colored by pLDDT.
18.01.2025 00:30 — 👍 17 🔁 3 💬 1 📌 1
Learn how to predict mono-, multi-mers and conformations with the ColabFold-AlphaFold2 protocol now out in @NatureProtocols. Right in time for the Nobel Prize! It covers workflows for beginners and advanced concepts.
🚀https://rdcu.be/dWViQ
📄https://www.nature.com/articles/s41596-024-01060-5 🧬🧶
14.10.2024 15:29 — 👍 17 🔁 8 💬 0 📌 0
Outer product mean should go from MSA to pair representation.
08.12.2024 23:43 — 👍 1 🔁 0 💬 0 📌 0
David Baker chats with Rosetta folks
Nobel Laureates in Chemistry David Baker, Demis Hassabis, and John Jumper
David Baker visits all the Rosetta folks after his Nobel lecture. And photo of all three Chemistry laureates - David Baker, Demis Hassabis, and John Jumper. An honor to be here in Stockholm to see this.
08.12.2024 12:47 — 👍 112 🔁 17 💬 1 📌 0
We updated our BindCraft preprint with lots of new exciting results! We release all our binder sequences and models, include more in silico analysis, novel design targets, and present AAV retargeting to specific cell types using de novo binders!
www.biorxiv.org/content/10.1...
08.12.2024 08:26 — 👍 128 🔁 31 💬 1 📌 3
Here is the performance of AlphaFold3-server vs. ColabFold-baseline on protein domains. AlphaFold3 is better for the majority of targets. I suspect that the weaker performance of AlphaFold3 in a couple of cases is due to using a reduced database for MSA construction.
01.12.2024 01:40 — 👍 9 🔁 1 💬 0 📌 0
Here is the plot for the protein complex predictions. AlphaFold3 server is an improvement over AlphaFold2 baseline represented by ColabFold. #CASP16
01.12.2024 00:21 — 👍 20 🔁 6 💬 1 📌 0
#CASP16 program is posted (so you can guess the "winners". Congratulations to Yang and Kihara who seems to have done well in RNA+Proteins. Also congratulations to AF3-server (i.e. me) who was selected to talk (i.e. most people did worse than the server). predictioncenter.org/casp16/doc/C... .
28.11.2024 07:39 — 👍 41 🔁 18 💬 2 📌 1
"There are no answers; only choices."
– S. Lem
I choose one [o] or two-cell [8] organisms and dissonant music.
Professor of Biochemistry @ UW-Seattle. Any coincidence of my opinions with my employer's is coincidental.
Husband, Father and grandfather, Datahound, Dog lover, Fan of Celtic music, Former NIGMS director, Former EiC of Science magazine, Stand Up for Science advisor, Pittsburgh, PA
NIH Dashboard: https://jeremymberg.github.io/jeremyberg.github.io/index.html
Microbiologist at UC Santa Cruz. Streptococcus pneumoniae, circadian rhythms, pneumonia, inflammation. www.kimmeylab.com
Interested in Structural Biology, deep learning, NextFlow, HPC, viruses, missense mutations archaea, bacteria, evolution & random quirks of nature. (Protein Cosmos feed 🧶🧬) Leads a research group & Structural biology Facility,UNSW Sydney. Opinions my own.
PhD student (close to finish!) at the University Würzburg. Likes to play with structure prediction tools, Crosslinking-MS, Native MS and bicycles. Proud of DOI:10.1073/pnas.2009502117 and DOI:10.1101/2024.04.30.591961 #TeamMassSpec #phdlife #peroxisomes
Professor of #structuralbiology at Newcastle University.
Heart says x-ray but mind starts to say EM.
#Drugdiscovery in #rarediseases, esp Inborn errors of metabolism
Yue Lab: https://www.staff.ncl.ac.uk/yuelab/
CNRS scientist computational molecular biology. Mostly talking about life, travel, science and board games, unless it's something else.
🇦🇺 Senior Lecturer at @sydneyuni.bsky.social and former NIHer. Research: Bacterial outer membrane biogenesis - membrane protein folding - protein translocation across membranes - novel antibiotics. He/him.
Staff Research Engineer in BioAI at InstaDeep (part of @biontech.bsky.social)- machine learning for personalized cancer vaccines, de novo peptide sequencing and signal peptides.
From Belgium 🇧🇪 currently living in Cape Town 🇿🇦
#bioML #TeamMassSpec
Tenure-track professor (PI) at Fudan University.
Have been working on motor protein, microtubule, and cilia.
Recently also working with membrane proteins.
Associate Editorial Board member of Cytoskeleton Journal.
Lab website: https://tinyurl.com/22c3eymy
Full stack developer who occasionally wears a lab coat. Graduate student at Harvard Medical School.
Director | Protein Structure, Analysis, & Design Core
Adj Assistant Professor | Molecular Physiology & Biophysics
University of Iowa
Structural Biology | Biophysical Characterization | Protein Design
Views are my own.
Open source methods for #metagenomics with @martinsteinegger.bsky.social Seoul National University 🇰🇷 | former Söding Lab MPI-NAT 🇩🇪 | http://mstdn.science/@milotmirdita
Molecular microbiologist studying bacterial nanomachines, Institut Pasteur, Paris
PhD student @MIT • Research on Generative Models for Biophysics and Drug Discovery
Associate Professor of Microbiology & Immunology. Scientist & Lab Leader. Streptococcus, invasive infection, host-pathogen interaction, cell death, antibiotic failure, academia, mentoring. Only my opinions
Senior AI Scientist at Absci (@abscibio)
Professor in bioinformatics, Stockholm University. Protein structure lover ( interactions predictions, evolution ..). Using machine learning as a part of AI for Sciences for halv my life. In addition to succén, I sometimes rants about sailing or skiing.
Mycobacteriologist and Postdoctoral Fellow in the York Bioenergetics Lab, University Of York (@jnb-lab.bsky.social).
Formerly: @pembroke1347.bsky.social & @mrclmb.bsky.social. @mcbseattle.bsky.social PhD.
Associate Professor, studies host-microbe interactions and women's health. Views are my own.
