Run AlphaFold in ChimeraX for cryoEM model building
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- เผยแพร่เมื่อ 20 ส.ค. 2024
- We show how to run AlphaFold from ChimeraX to predict a protein structure from its sequence to produce an initial model for building into a 3 Angstrom resolution cryoEM map. We look at a protein that transports omega-3 fatty acids across the blood-brain barrier, EMDB 23883. Requires ChimeraX 1.3 or a daily build newer than September 2021.
Hello, It is wonderful information you gave thank you. Could you please also provide some info or video on how to perform this same funtion if we have multi-domian herto protein structure with 2 or more subunits? will the same protocol can be applicable in that case or we need to apply some different strategy?
AlphaFold works on a single protein sequence. I have heard people try to put a linker between two proteins to make it a single sequence and then run AlphaFold with mixed results. I would not expect that to work well because the multiple sequence alignment AlphaFold produces to predict the long range contacts won't include sequences spanning the linker so I would not think it would provide any info about inter-protein contacts. Also AlphaFold crashes on longer sequences running out of GPU memory. The EBI AlphaFold database limited sequences to 1400 amino acids and that used the memory from 4 GPUs. The ChimeraX AlphaFold prediction can only use one GPU and seems limited to about 800 amino acids.
Very nice!