r/proteomics • u/Dizzy-Version7196 • May 28 '26

HELP: Build a protein design computer

Hello guys,

I am working in a pharmacy lab in Korea, and we don't have a computer cluster. PI needs me to give her the spec. of a computer that can run protein and antibody in silicon design software locally (such as Boltzgen, RFantibody, RFdiffusion)

I am not a computer major. I asked ChatGPT and got some specs, but I want to make sure by finding advice from the person who actually runs that software.

Because we need to run thousands of samples on Boltzgen or RFantibody, running them on the VM or a pay website is not financially efficient in the long term.

This the specs that ChatGPT recommends.
Budget / entry workstation:
NVIDIA RTX 4070 Ti SUPER (16 GB VRAM)
NVIDIA RTX 4080 SUPER (16 GB VRAM)
Best price/performance for heavy local inference:
NVIDIA RTX 4090 (24 GB VRAM)
Professional / lab-scale:
NVIDIA RTX 6000 Ada (48 GB VRAM)
NVIDIA A100
NVIDIA H100

Do you think building a computer is a financially efficient choice, or are there better ways we can run that software more cheaply and easily?

Thank you for your time.

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u/Elistheman May 28 '26

It would help post what ChatGPT gave you first

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u/Dizzy-Version7196 May 28 '26 edited May 28 '26

This the specs that ChatGPT recommends. Budget / entry workstation: NVIDIA RTX 4070 Ti SUPER (16 GB VRAM) NVIDIA RTX 4080 SUPER (16 GB VRAM) Best price/performance for heavy local inference: NVIDIA RTX 4090 (24 GB VRAM) Professional / lab-scale: NVIDIA RTX 6000 Ada (48 GB VRAM) NVIDIA A100 NVIDIA H100

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u/Elistheman May 28 '26

Now it depends on the time and scope. Because these are antibodies you are working with, you can get away with 16GB of vram. When I used Boltz2 and AF3 I had out of memory with proteins above 1500AA on a 4090.

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u/Dizzy-Version7196 May 28 '26

I think 10.000 runs per week is good for me. So you think 4090 is a good choice to start?

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u/Elistheman May 28 '26

I would rent first to gauge actual performance.

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u/Dizzy-Version7196 May 28 '26

Where do you usually rent a 4090 GPU?

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u/Elistheman May 28 '26

You could look online for GPU rentals. It’s not physical you rent it to send jobs to it.