11 citations · 12 across the 3 of their papers we have counts for
4 papers
StabilityArc: Decoding Protein Sequence Embeddings into Generalizable Stability Landscapes
Aaron L. Feller, Andrew D. Ellington, Claus O. Wilke
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, train…
EnsembleEGNN: Set-Based Graph Learning for Thermodynamic Ensembles of Cyclic Peptides
Aaron L. Feller, Aaron Feller, Kris Deibler +1
Molecular graph encoding often relies on a single, static structure, ignoring the thermodynamic ensemble of molecules that are present in solution. Here, we introduce EnsembleEGNN,…
p2smi: A Python Toolkit for Peptide FASTA-to-SMILES Conversion and Molecular Property Analysis
Aaron L. Feller, Claus O. Wilke
Converting peptide sequences into useful representations for downstream analysis is a common step in computational modeling and cheminformatics. Furthermore, peptide drugs (e.g., S…
Prompt Engineering for Transformer-based Chemical Similarity Search Identifies Structurally Distinct Functional Analogues
Clayton W. Kosonocky, Aaron L. Feller, Claus O. Wilke +1
Chemical similarity searches are widely used in-silico methods for identifying new drug-like molecules. These methods have historically relied on structure-based comparisons to com…