Author

Artem Y. Lyubimov

University of California, San FranciscoORCID 0000-0002-2089-1870Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Biochemistry· 1 Bioengineering· 1 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Assay:protein structure· 2 Research Focus:protein structure prediction· 2 Approach:diffusion model· 1 Research Focus:drug response / drug discovery· 1 Approach:experimental assay· 1 Research Focus:perturbation response prediction· 1 Research Focus:protein design· 1

Frequent Co-Authors

James S. FraseriD· 2 shared Aaron S. BrewsteriD· 1 shared Aaron S. PetruzzellaiD· 1 shared Adrian W. DobbelsteiniD· 1 shared Aina E. CoheniD· 1 shared Ana R. Lemos· 1 shared Arne SchneuingiD· 1 shared Asmit BhowmickiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 19 mutual co-author links

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2 shared papersBioinformatics

James S. FraserORCID

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Author profile →

3 papers

Recent·Most cited

A Unified 3D Generative Model for Synthesizable Structure-Based Drug Design

Ilia Igashov, Arne Schneuing, Adrian W. Dobbelstein, Irina Morozova, Rebecca M. Neeser, Kara Zielinski, Luciano A. Abriata, Aaron S. Petruzzella, David Robin Pavel Iosub, Olivia Gampp, Artem Y. Lyubimov, Evgenia Elizarova, Isabella Ferrara, Pedro M. F. Sousa, Ana R. Lemos, , Bruno E. Correia

This paper introduces LDDM, a generative model for drug design that produces synthetically accessible compounds validated experimentally for five protein targets.

bioRxiv · Sep 18, 2026 · PreprintBioinformatics

Programming protein shape as an explicit design layer via CAD blueprint-guided diffusion

Yilun Qi, Guoxun Zhang, Klaus Yserentant, Sonya Lee, Artem Y. Lyubimov, Kyrellos E. Ibrahim, Giuseppe Cimicata, James S. Fraser, Bo Huang, Tanja Kortemme

The paper integrates CAD blueprints with diffusion models to explicitly program protein shapes, demonstrating emergent functions through molecular design.

bioRxiv · Jul 23, 2026 · PreprintBioengineering

Structure of active methyl-CoM reductase, Earth's main methane producer

Christopher J. Ohmer, Macon J. Abernathy, Darya Marchany‐Rivera, David G. Villareal, Philipp S. Simon, Artem Y. Lyubimov, Asmit Bhowmick, Kuntal Chatterjee, Hiroki Makita, Vandana Tiwari, Medhanjali Dasgupta, Stephen J. Keable, David Moreau, Daniel W. Paley⧓, Nigel W. Moriarty, , Stephen Wiley Ragsdale

The paper determines the structure of active Ni(I)-Methyl-CoM reductase, revealing how it catalyzes methane formation and providing insights for methane emission control and biofuel production.

bioRxiv · Apr 26, 2025 · PreprintBiochemistry