Related papers: Structure-based drug design by denoising voxel gri…

An important problem in the analysis of high-dimensional omics data is to identify subsets of molecular variables that are associated with a phenotype of interest. This requires addressing the challenges of high dimensionality, strong…

Evaluating code generation models for 3D spatial reasoning requires executing generated code in realistic environments and assessing outputs beyond surface-level correctness. We introduce a platform VoxelCode, for analyzing code generation…

Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a…

As the size of accessible compound libraries expands to over 10 billion, the need for more efficient structure-based virtual screening methods is emerging. Different pre-screening methods have been developed for rapid screening, but there…

Currently, the field of structure-based drug design is dominated by three main types of algorithms: search-based algorithms, deep generative models, and reinforcement learning. While existing works have typically focused on comparing models…

Deep generative models for graphs have exhibited promising performance in ever-increasing domains such as design of molecules (i.e, graph of atoms) and structure prediction of proteins (i.e., graph of amino acids). Existing work typically…

Structure-based drug design (SBDD) leverages the three-dimensional geometry of proteins to identify potential drug candidates. Traditional approaches, rooted in physicochemical modeling and domain expertise, are often resource-intensive.…

Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…

Denoising diffusion models have shown great potential in multiple research areas. Existing diffusion-based generative methods on de novo 3D molecule generation face two major challenges. Since majority heavy atoms in molecules allow…

Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…

State-of-the-art models for 3D molecular generation are based on significant inductive biases, SE(3), permutation equivariance to respect symmetry and graph message-passing networks to capture local chemistry, yet the generated molecules…

The need for advanced materials has led to the development of complex, multi-component alloys or solid-solution alloys. These materials have shown exceptional properties like strength, toughness, ductility, electrical and electronic…

Controllable molecular graph generation is essential for material and drug discovery, where generated molecules must satisfy diverse property constraints. While recent advances in graph diffusion models have improved generation quality,…

Understanding the structure of a protein complex is crucial indetermining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional.…

Structure-Based Drug Design (SBDD) is a powerful strategy in computational drug discovery, utilizing three-dimensional protein structures to guide the design of molecules with improved binding affinity. However, capturing complex…

We present XCube (abbreviated as $\mathcal{X}^3$), a novel generative model for high-resolution sparse 3D voxel grids with arbitrary attributes. Our model can generate millions of voxels with a finest effective resolution of up to $1024^3$…

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the…

Traditional drug discovery relies on rounds of screening millions of candidate molecules with low success rates, making drug discovery time and resource intensive. To overcome this screening bottleneck, we introduce Latent-X, an all-atom…

We present a novel diffusion-based framework for synthesizing 2D vector fields from sparse, coherent inputs (i.e., streamlines) while maintaining physical plausibility. Our method employs a conditional denoising diffusion probabilistic…

Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional methods for identifying "hit" molecules from a large…