Many all-atom generative protein models can in principle design large multimeric complexes by jointly modelling all chains, but their quadratic token- and atom-pair representations quickly exceed single-GPU memory as the number of chains and residues modelled grows. We introduce Design-CP, two context-parallel (CP) inference strategies for RFdiffusion 3 (1D row-sharding and 2D grid sharding with ring attention) that distribute the quadratic activations across a multi-GPU mesh while preserving pretrained weights. We characterise their scaling when sampling icosahedral assemblies, showing that the maximum feasible asymmetric subunit (ASU) size grows with the expected square-root trend in GPU count and that 2D sharding achieves better wall-clock scaling. Moreover, we show how strong point-group symmetry constraints make CP usable out of the box for end-to-end, all-atom design of icosahedral nanoparticles, yielding favourable in silico structural and interface metrics. Finally, we demonstrate octahedral nanoparticle design on a small cluster of workstation-grade 16GB GPUs, illustrating how Design-CP can be a practical path towards democratising large-assembly protein design.
The ability to generate variable-length proteins is crucial in protein design, where the optimal length is often unknown and tightly coupled to designability. Current diffusion- and flow-based generative models typically require the protein length to be specified before sampling,…
In this paper, we aim to combine the advantages of existing sequence parallelism paradigms and overcomes their drawbacks, the most serious of which is the incapability to correctly compute causal attention on the hybrid-context packed sequences, in a stronger sequence parallelism…
Predicting biomolecular properties from limited labeled data is a central bottleneck in protein engineering and small-molecule design. As strong pretrained encoders now supply rich fixed-length representations, the difficulty has shifted from representation learning to building a…
Training large language models at the multi-billion to trillion parameter scale is confined to datacenters, where data-parallel (DP) and model-parallel (MP) techniques presume homogeneous accelerators, high-speed interconnects, and a single orchestrating entity. Frontier model de…
The silhouette is one of the most widely used measures to assess the quality of a $k$-clustering of a dataset of $n$ elements. Its evaluation requires no information beyond the clustering assignment. In addition, the silhouette is extremely easy to interpret, providing a score to…
Current computational approaches for drug design typically focus on generating molecules conditioned on specific targets or general molecular properties, often neglecting the influence of disease context on target behavior and therapeutic outcomes. To address this gap, we introdu…