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physics.bio-ph2025
Dummy Atom Based Thermodynamic Integration Accurately Predicts Disulfide Redox Free Energies in Proteins
Daniel Mejia-Rodriguez, Suman Samantray, Margaret S. Cheung +1
A thermodynamic integration (TI) protocol incorporating dummy atoms is introduced to calculate free energy differences for disulfide bond formation in proteins. This method success…
physics.bio-ph2025
PTM-Psi on the Cloud
Suman Samantray, Margot Lockwood, Amity Andersen +4
We developed an advanced computational framework to accelerate the study of the impact of post-translational modifications on protein structures and interactions (PTM-Psi) using as…