Vilya-1: An all-atom foundation model for macrocycle structure prediction and design
2026-07-10 • Machine Learning
Machine Learning
AI summaryⓘ
The authors present Vilya-1, a deep learning tool designed to predict the shapes and important properties of macrocyclic peptides, which are increasingly used as medicines. Unlike older methods, Vilya-1 works well across many different types of these molecules, including unusual ones, by learning from diverse data. It predicts structures more accurately than traditional physics-based or existing AI methods and can also help create new macrocycles with desired features. This makes Vilya-1 a useful tool for designing new peptide-based drugs.
macrocyclic peptidesdeep learningconformation samplingmembrane permeabilityall-atom representationcanonical residuesnon-canonical residuesgenerative modeldrug developmentstructural prediction
Authors
Vilya Research, :, Pascal Sturmfels, Milad Salem, Naozumi Hiranuma, Stephen Rettie, Xiaoliang Pan, Benjamin D. Sellers, Adam P. Moyer, Patrick J. Salveson, Ivan Anishchanka
Abstract
Macrocyclic peptides are an increasingly important therapeutic modality, but existing computational methods for modeling their structures and properties are limited in scope and do not generalize well across the synthetically accessible chemical space. In this work, we introduce Vilya-1, a deep learning model that addresses two central challenges in macrocycle design: sampling biologically relevant conformations across arbitrary chemistries and predicting key developability properties such as membrane permeability. Vilya-1 operates on a uniform all-atom representation and is trained on heterogeneous structural datasets spanning diverse topologies and chemical classes. Across a broad set of macrocycles composed of canonical and non-canonical residues, Vilya-1 substantially improves geometric accuracy relative to physics-based methods, co-folding networks, and deep-learning conformer generators, while maintaining broad chemical coverage that extends to small molecules. Vilya-1 also supports generative applications, enabling the design of novel macrocycles with tailored chemical, structural, and property profiles. Together, these capabilities establish Vilya-1 as a foundation model for accelerating the development of next-generation macrocycle therapeutics.