bioRxivBioinformaticsPreprint
Efficient protein structure prediction fromcompact computers to datacenters withOpenFold-TRT
Kieran DidiiD, Prashant SohaniiD, Fabian BerressemiD, Alexander Nesterovskiy, Boris Fomitchev, Robert Ohannessian, Mohamed Elbalkini, Jonathan Cogan, Anthony B. CostaiD, Arash VahdatiD, Felix KallenborniD, Bertil SchmidtiD, Milot MirditaiD, Martin SteineggeriD, Christian DallagoiD, Alejandro ChacóniD
Abstract
We introduce accelerations for deep learning inference with OpenFold and TensorRT that, combined with MMseqs2-GPU on an x86 system with one NVIDIA RTX PRO 6000 Blackwell Server Edition GPU, reach up to 131x faster inference compared to AlphaFold2. ARM-optimizations enable homology search on power efficient DGX Spark, and allow search beyond available GPU RAM on NVIDIA Grace Hopper Superchip at comparable overall folding speed. These accelerations enable high-throughput protein structure inference at no accuracy cost using familiar tools.
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