Paweł Gniewek

Dejun Lin, Simon Chu, Vishanth Iyer et al.

Understanding cellular machinery requires atomic-scale reconstruction of large biomolecular assemblies. However, predicting the structures of these systems has been constrained by hardware memory requirements of models like AlphaFold 3, imposing a practical ceiling of a few thousand residues that can be processed on a single GPU. Here we present NVIDIA BioNeMo Fold-CP, a context parallelism framework that overcomes this barrier by distributing the inference and training pipelines of co-folding models across multiple GPUs. We use the Boltz models as open source reference architectures and implement custom multidimensional primitives that efficiently parallelize both the dense triangular updates and the irregular, data-dependent pattern of window-batched local attention. Our approach achieves efficient memory scaling; for an N-token input distributed across P GPUs, per-device memory scales as $O(N^2/P)$, enabling the structure prediction of assemblies exceeding 30,000 residues on 64 NVIDIA B300 GPUs. We demonstrate the scientific utility of this approach through successful developer use cases: Fold-CP enabled the scoring of over 90% of Comprehensive Resource of Mammalian protein complexes (CORUM) database, as well as folding of disease-relevant PI4KA lipid kinase complex bound to an intrinsically disordered region without cropping. By providing a scalable pathway for modeling massive systems with full global context, Fold-CP represents a significant step toward the realization of a virtual cell.

Aryan Pedawi, Pawel Gniewek, Chaoyi Chang et al.

Virtual, make-on-demand chemical libraries have transformed early-stage drug discovery by unlocking vast, synthetically accessible regions of chemical space. Recent years have witnessed rapid growth in these libraries from millions to trillions of compounds, hiding undiscovered, potent hits for a variety of therapeutic targets. However, they are quickly approaching a size beyond that which permits explicit enumeration, presenting new challenges for virtual screening. To overcome these challenges, we propose the Combinatorial Synthesis Library Variational Auto-Encoder (CSLVAE). The proposed generative model represents such libraries as a differentiable, hierarchically-organized database. Given a compound from the library, the molecular encoder constructs a query for retrieval, which is utilized by the molecular decoder to reconstruct the compound by first decoding its chemical reaction and subsequently decoding its reactants. Our design minimizes autoregression in the decoder, facilitating the generation of large, valid molecular graphs. Our method performs fast and parallel batch inference for ultra-large synthesis libraries, enabling a number of important applications in early-stage drug discovery. Compounds proposed by our method are guaranteed to be in the library, and thus synthetically and cost-effectively accessible. Importantly, CSLVAE can encode out-of-library compounds and search for in-library analogues. In experiments, we demonstrate the capabilities of the proposed method in the navigation of massive combinatorial synthesis libraries.