A new age in protein design empowered by deep learning

H Khakzad, I Igashov, A Schneuing, C Goverde… - Cell Systems, 2023 - cell.com
The rapid progress in the field of deep learning has had a significant impact on protein
design. Deep learning methods have recently produced a breakthrough in protein structure …

De novo design of protein structure and function with RFdiffusion

JL Watson, D Juergens, NR Bennett, BL Trippe, J Yim… - Nature, 2023 - nature.com
There has been considerable recent progress in designing new proteins using deep-
learning methods,,,,,,,–. Despite this progress, a general deep-learning framework for protein …

Diffdock: Diffusion steps, twists, and turns for molecular docking

G Corso, H Stärk, B **g, R Barzilay… - arxiv preprint arxiv …, 2022 - arxiv.org
Predicting the binding structure of a small molecule ligand to a protein--a task known as
molecular docking--is critical to drug design. Recent deep learning methods that treat …

Antigen-specific antibody design and optimization with diffusion-based generative models for protein structures

S Luo, Y Su, X Peng, S Wang… - Advances in Neural …, 2022 - proceedings.neurips.cc
Antibodies are immune system proteins that protect the host by binding to specific antigens
such as viruses and bacteria. The binding between antibodies and antigens is mainly …

SE (3) diffusion model with application to protein backbone generation

J Yim, BL Trippe, V De Bortoli, E Mathieu… - arxiv preprint arxiv …, 2023 - arxiv.org
The design of novel protein structures remains a challenge in protein engineering for
applications across biomedicine and chemistry. In this line of work, a diffusion model over …

Antigen-specific antibody design via direct energy-based preference optimization

X Zhou, D Xue, R Chen, Z Zheng… - Advances in Neural …, 2025 - proceedings.neurips.cc
Antibody design, a crucial task with significant implications across various disciplines such
as therapeutics and biology, presents considerable challenges due to its intricate nature. In …

Diffusion models in protein structure and docking

J Yim, H Stärk, G Corso, B **g… - Wiley …, 2024 - Wiley Online Library
Generative AI is rapidly transforming the frontier of research in computational structural
biology. Indeed, recent successes have substantially advanced protein design and drug …

Se (3) diffusion model-based point cloud registration for robust 6d object pose estimation

H Jiang, M Salzmann, Z Dang… - Advances in Neural …, 2023 - proceedings.neurips.cc
In this paper, we introduce an SE (3) diffusion model-based point cloud registration
framework for 6D object pose estimation in real-world scenarios. Our approach formulates …

Mirror diffusion models for constrained and watermarked generation

GH Liu, T Chen, E Theodorou… - Advances in Neural …, 2023 - proceedings.neurips.cc
Modern successes of diffusion models in learning complex, high-dimensional data
distributions are attributed, in part, to their capability to construct diffusion processes with …

Towards predicting equilibrium distributions for molecular systems with deep learning

S Zheng, J He, C Liu, Y Shi, Z Lu, W Feng, F Ju… - arxiv preprint arxiv …, 2023 - arxiv.org
Advances in deep learning have greatly improved structure prediction of molecules.
However, many macroscopic observations that are important for real-world applications are …