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Structure determination is essential to a mechanistic understanding of diseases and the development of novel therapeutics. Machine-learning-based structure prediction methods have made significant advancements by computationally predicting…

Contact-assisted protein folding has made very good progress, but two challenges remain. One is accurate contact prediction for proteins lack of many sequence homologs and the other is that time-consuming folding simulation is often needed…

Designing ligand-binding proteins, such as enzymes and biosensors, is essential in bioengineering and protein biology. One critical step in this process involves designing protein pockets, the protein interface binding with the ligand.…

Understanding the structure of the protein-ligand complex is crucial to drug development. Existing virtual structure measurement and screening methods are dominated by docking and its derived methods combined with deep learning. However,…

We present a novel way to predict molecular conformers through a simple formulation that sidesteps many of the heuristics of prior works and achieves state of the art results by using the advantages of scale. By training a diffusion…

Diffusion models have shown exceptional performance in visual generation tasks. Recently, these models have shifted from traditional U-Shaped CNN-Attention hybrid structures to fully transformer-based isotropic architectures. While these…

Structure-informed protein representation learning is essential for effective protein function annotation and \textit{de novo} design. However, the presence of inherent noise in both crystal and AlphaFold-predicted structures poses…

We present a latent diffusion model for fast feed-forward 3D scene generation. Given one or more images, our model Bolt3D directly samples a 3D scene representation in less than seven seconds on a single GPU. We achieve this by leveraging…

Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale,…

Monocular 3D pose estimation is fundamentally ill-posed due to depth ambiguity and occlusions, thereby motivating probabilistic methods that generate multiple plausible 3D pose hypotheses. In particular, diffusion-based models have recently…

Despite recent advancement in 3D molecule conformation generation driven by diffusion models, its high computational cost in iterative diffusion/denoising process limits its application. In this paper, an equivariant consistency model…

The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on…

Diffusion model deployment has been suffering from high energy consumption and inference latency despite its superior performance in visual generation tasks. Dynamic voltage and frequency scaling (DVFS) offers a promising solution to…

Deep generative models have achieved tremendous success in structure-based drug design in recent years, especially for generating 3D ligand molecules that bind to specific protein pocket. Notably, diffusion models have transformed ligand…

The rapid progress of large multimodal models has inspired efforts toward unified frameworks that couple understanding and generation. While such paradigms have shown remarkable success in 2D, extending them to 3D remains largely…

Diffusion models have achieved impressive generative quality across modalities like 2D images, videos, and 3D shapes, but their inference remains computationally expensive due to the iterative denoising process. While recent caching-based…

This chapter deals with approaches for protein three-dimensional structure prediction, starting out from a single input sequence with unknown struc- ture, the 'query' or 'target' sequence. Both template based and template free modelling…

Garment sewing patterns are fundamental design elements that bridge the gap between design concepts and practical manufacturing. The generative modeling of sewing patterns is crucial for creating diversified garments. However, existing…

Stabilizing proteins is a foundational step in protein engineering. However, the evolutionary pressure of all extant proteins makes identifying the scarce number of mutations that will improve thermodynamic stability challenging. Deep…

We present an investigation into diffusion models for molecular generation, with the aim of better understanding how their predictions compare to the results of physics-based calculations. The investigation into these models is driven by…