#af2 — Public Fediverse posts

USAF C-32A 99-0004 as Air Force 2 with the twilight reflected along her length departs Moffett Field, Sunnyvale, California May 16th, 2025 #USAF #C32A #AF2 #VPOTUS #KNUQ #Moffett #twilight #militaryaviation #AvGeek #spotter #photography #aircraft #milair #nikon

Using #ChimeraX, I dock these #AF2 models into the map. I have seen a case with two different protein subunits of very similar sequences, which makes assigning each AF2 model to the density pretty difficult. It is however very easy to align (with the `matchmaker` command in ChimeraX) the AF2 models to the model produced by #model_angelo. This will unambiguously place similar AF2 models to where model_angelo detected their sequences.
5/19

Having identified the proteins, I fetch their #AlphaFold2 predictions from AlphaFold-DB, or compute them if not in the DB. #AF2 models have excellent geometry and complete sequence correctly numbered, so they are excellent starting models. I rarely use #PDB entries as starting models anymore. Rare exceptions: a PDB entry I deposited myself, or one containing a post-translational modification or non-natural amino acid I need (never present in #AF2 models, only the 20 standards amino acids).
4/19

#SaprotHub: Making #protein #modeling accessible to all biologists:

-create & train own #DeepLearning models without the need for advanced #MachineLearning & coding expertise

https://doi.org/10.1101/2024.05.24.595648
#DIYbio #bioinformatics #CompChem #AI #ML #KI #LLM #AF2 #ESMfold #ColabFold #sciece #research