Toward deep learning sequence–structure co-generation for protein design

C Wang, S Alamdari, C Domingo-Enrich… - Current Opinion in …, 2025 - Elsevier
Highlights•Deep generative models generate proteins to help solve modern-day
challenges.•Most generative models of proteins generate sequences directly or generate …

Computational protein design

KI Albanese, S Barbe, S Tagami… - Nature Reviews …, 2025 - nature.com
Combining molecular modelling, machine-learned models and an increasingly detailed
understanding of protein chemistry and physics, computational protein design and human …

[HTML][HTML] Challenges and compromises: Predicting unbound antibody structures with deep learning

A Greenshields-Watson, O Vavourakis… - Current Opinion in …, 2025 - Elsevier
Therapeutic antibodies are manufactured, stored and administered in the free state; this
makes understanding the unbound form key to designing and improving development …

The Superposition of Diffusion Models Using the It\^ o Density Estimator

M Skreta, L Atanackovic, AJ Bose, A Tong… - arxiv preprint arxiv …, 2024 - arxiv.org
The Cambrian explosion of easily accessible pre-trained diffusion models suggests a
demand for methods that combine multiple different pre-trained diffusion models without …

Scalable emulation of protein equilibrium ensembles with generative deep learning

S Lewis, T Hempel, J Jiménez-Luna, M Gastegger… - bioRxiv, 2024 - biorxiv.org
Following the sequence and structure revolutions, predicting the dynamical mechanisms of
proteins that implement biological function remains an outstanding scientific challenge …

Outsourced diffusion sampling: Efficient posterior inference in latent spaces of generative models

S Venkatraman, M Hasan, M Kim, L Scimeca… - arxiv preprint arxiv …, 2025 - arxiv.org
Any well-behaved generative model over a variable $\mathbf {x} $ can be expressed as a
deterministic transformation of an exogenous ('outsourced') Gaussian noise variable …