Latest posts tagged with #AF3 on Bluesky
#GoogleCloudDay bits. Kudos to Nikos Tzollas, Triantafyllos Karathanasis, Viktoria Kalfaki, Katerina Tzouvara. At @katsilalab.bsky.social , our AI-Enhanced Ligand–Receptor Profiling for Drug Repurposing is built upon #AF3 structural predictions to accelerate mechanism-driven #drug #repurposing
This explains why deleting a chunk of the linker between the pUL21 N-terminal domain (NTD) and the TROPPO motifs abolishes PP1 binding, why our previous TROPPO mutations prevent binding (they would block packing of the TROPPO and the pUL21 NTD), and new mutations further supported the #AF3 models.
This sounds interesting and maybe exactly what I need. Plan to di some screening with #AF3 and a proper implementation ofna scoring function was still missing 👍 thanks!
Important #AlphaFoldology thread about scoring intramolecular complexes in #AF2 and #AF3
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.
#CASP ligand #Alphafoldology - #AF3 wins over all other methods in baseline ligand prediction…
Nice quick #Alphafoldology review of #AF3 clones.
Comparison of #AF3 clone codebases according to Gemini
#Alphafoldology #Boltz-1 #Chai-1 #Protenix
When #alphafold #AF3 gives you 3 very different interfaces with equivalent low confidence scores that do not allow you to discriminate between each and only the experimental structure allows you to know which AF3 model is the right one, not really useful. 😂
#alphafold #alphafold3
Some models are very weird (hallucination) and do not make sense at all.
As always, use #AF3 with caution, and consult your friendly structural biologist to help you interpret the results.
#alphafold #AF3
modelling 2 transcription factors (full length) bound to their cognate binding sites.
DBDs looks OK but for the rest 🤪
#Alphafold #AF3
not accurate in predicting interaction between a nanobody and its target
Top : right structure (PDB 6H02) with the nanobody in cyan
Bottom : 5 AF3 models
Some light reading for tonight... Jokes apart, this is really great progress. A bit unfortunate that it's locked behind a server. The best part about AF2 was the whole suite of tools and packages that folks built on top of AF2
#AF3 #compchemsky #chemsky
