T. Simonson

Redesigning methionyl-tRNA synthetase for β-methionine activity with adaptive landscape flattening and experiments

The paper redesigns methionyl-tRNA synthetase to increase activity towards β-methionine using computational protein design and experimental validation.

A physics-based energy function allows the computational redesign of a PDZ domain

This paper redesigns a PDZ domain using a physics-based energy function, showing that sequences generated by Monte Carlo simulations can fold into the correct structure and bind ligands.

Proteus software for physics-based protein design

The paper introduces Proteus, a software tool for physics-based protein design, demonstrating its effectiveness in redesigning PDZ domains and enzymes with specific functional properties.

Adaptive landscape flattening allows the design of both enzyme:substrate binding and catalytic power

This paper designs an enzyme to bind transition state analogs using adaptive landscape flattening, achieving accurate predictions of catalytic activity and reaction rates.