Bruce Randall Donald

The paper measures folding thermodynamics of SpA domains and identifies a stability gradient that facilitates efficient secretion.

The paper introduces CCK*, a suite of algorithms for de novo design of L- and D-peptides, integrating data-driven and physics-based methods to expand design space across chiral spaces.

The paper evaluates computational methods for predicting interdomain pose distributions in D-L-D proteins using NMR and SAXS data, finding none accurately match experimental results.

The paper introduces PATH, an interpretable algorithm for predicting protein-ligand binding affinity using persistent homology, achieving comparable performance with reduced computational complexity.

This paper evaluates AlphaFold 3's ability to predict D-peptide chirality, fold, and binding pose in heterochiral complexes and finds it performs poorly, with a high chirality violation rate.

DexDesign is a new OSPREY-based algorithm for designing D-peptide inhibitors targeting PDZ domains, generating peptides predicted to bind tighter than endogenous ligands.

RO_SCPLOWESISTORC_SCPLOW predicts resistance mutations by optimizing four criteria using Pareto frontiers, identifying clinically relevant mutations in EGFR and BRAF inhibitors.

OSPREY 3.0 improves protein design software with faster algorithms, GPU support, and a Python interface, showing accurate mutation effect predictions on protein-protein binding.