Author

Aaron L. Feller

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#machine learning Preprint Sep 2026

StabilityArc: Decoding Protein Sequence Embeddings into Generalizable Stability Landscapes

Every protein has a unique stability landscape, but the physical consequences of mutation are governed by recurring biochemical constraints. We test whether a shared decoder, trained on measurements from diverse proteins, can interpret these constraints in an unseen target, enabling cross-protein transfer for initial e...

Aaron L. Feller, Andrew D. Ellington, Claus O. Wilke · 0 citations

#machine learning Preprint Jul 2026

Graph Learning on Ensembles of Cyclic Peptides: An Investigation of Molecular Ensemble Modeling

It is demonstrated that encoding conformational ensembles into a single thermodynamically informed embedding improves cyclic-peptide property prediction.

Aaron L. Feller, Kristine Deibler, Maxim Secor · 0 citations

Open access Aug 2026

Combining Machine Learning and Directed Evolution for Optimization of a Monooxygenase

A systematic comparison of zero-shot ML models is provided and an iterative framework for integrating machine learning with directed evolution to accelerate enzyme engineering is established to accelerate enzyme engineering.

Daniel Gutierrez, Isa Madrigal Harrison, Aaron L. Feller et al. · bioRxiv · 0 citations