Best GPU for local AlphaFold
Author: David458-altCreated Apr 30, 2026Updated Apr 30, 2026
Hello,
I’m planning a workstation to run AlphaFold locally and need advice on GPU choice.
My use case: Prediction of ~10,000 proteins (750–1500 aa)
I’m considering:
RTX 4090 (24 GB) RTX 5090 (~32 GB) RTX 6000 Ada (48 GB)
Questions:
Any experience with these GPUs for AlphaFold or other models like PLACER, RFDiffussion and LigandMPNN? Better to go with one RTX 6000 or multiple 4090s?
Thanks!
Source: google-deepmind/alphafold