Vilya-1: An all-atom foundation model for macrocycle structure prediction and design
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Computer Science > Machine Learning
arXiv:2607.09998 (cs)
[Submitted on 10 Jul 2026]
Title:Vilya-1: An all-atom foundation model for macrocycle structure prediction and design
Authors:Vilya Research: Pascal Sturmfels, Milad Salem, Naozumi Hiranuma, Stephen Rettie, Xiaoliang Pan, Benjamin D. Sellers, Adam P. Moyer, Patrick J. Salveson, Ivan Anishchanka
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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.
| Comments: | 21 pages, 14 figures |
| Subjects: | Machine Learning (cs.LG); Biomolecules (q-bio.BM) |
| Cite as: | arXiv:2607.09998 [cs.LG] |
| (or arXiv:2607.09998v1 [cs.LG] for this version) | |
| https://doi.org/10.48550/arXiv.2607.09998
arXiv-issued DOI via DataCite (pending registration)
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