Accelerating End-to-End Co-Folding Performance with NVIDIA BioNeMo Agent Toolkit | NVIDIA Technical Blog

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This post details the acceleration of end-to-end co-folding performance using the NVIDIA BioNeMo Agent Toolkit. It highlights specific optimizations for each stage of the biomolecular structure prediction pipeline: MMseqs2-GPU for MSA generation (up to 177x faster than CPU JackHMMER), cuEquivariance for co-folding inference (up to 3x faster and extending sequence length to ~5.9k tokens), and further optimizations via the OpenFold3 NIM (up to 6,400 tokens on a single B300). It also introduces Fold-CP for context-parallel inference, enabling the modeling of large assemblies (up to 32,000 tokens on 64 B300 GPUs). These components are orchestrated by the BioNeMo Agent Toolkit, demonstrating an end-to-end accelerated workflow for drug discovery and protein design.