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Updated: Oct 3, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
A machine learning method for calculating highly localized protein stabilities
Chenlin Lu1, Kyle C Weber1, Savannah K McBride1
1Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
Abstract:
The residue-level free energy of opening (∆Gop) is the thermodynamic descriptor of localized protein stability, providing valuable information about the protein ensemble at physiologically relevant timescales and conditions. PFNet instantly determines ∆Gop for arbitrarily large proteins and complexes from conventional peptide-level hydrogen exchange-mass spectrometry (HX-MS) datasets. It unlocks the full potential of HX-MS, democratizing the method and establishing quantitative, scalable and accessible analysis.
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