We are a team of scientists working at the intersection of chemistry, biology, physics, medicine, and computer science. Our goal is to accelerate biomedical discovery and materials innovation through the development and application of simulation and data science tools.

We have contributed new tools and knowledge in several topic areas:

- mechanisms of pH-responsive materials based on surfactant and polysaccharide;

- pH-dependent structure-dynamics-function relationships in enzymes;

- proton-coupled conformational allostery;

- pH-dependent binding free energy calculations;

- mechanisms of proton-coupled channels and transporters;

- covalent drug design.

Current aims include:

- development of constant pH molecular dynamics techniques; 

- understanding proton-coupled ion and substrate transport across biological membrane;

- structure-based drug design targeting proteases and kinases;

- design of smart materials for medical and technological applications.

Recent highlights:


Accelerating targeted covalent kinase inhibitor design

Liu, Yue,& Shen, J Am Chem Soc 2019.

A molecular dynamics tool put to test for discovering covalent hotspots in kinases and other drug targets

Continuous constant pH molecular dynamics released in Amber18

Huang, Harris, et al., J Chem Inf Model 2018.

A new implementation for rapid and accurate pKa predictions and proton-coupled dynamics

Modern materials: responsive, 

reconfigurable, multi-functional

Tsai, Payne & Shen, Chem Mater 2018.

Exploiting a pKa gradient for persistent but erasable gradient in structural and mechanical properties