Research Areas

Our research lies at the intersection of structural biology, drug discovery, AI, and supercomputing. We leverage advanced computational methods and state-of-the-art supercomputers to solve complex biological problems. In the best of the days we arrive at new pictures of an important biological system, obtain experimental data to support them, and establish a pragmatic path for drug discovery.

1. Protein Conformational Dynamics

We utilize ultra-long timescale molecular dynamics (MD) as our primary tool to explore the intricate conformational dynamics of proteins. AI is crucial to better understanding the rich MD data, and the accumulation MD data over time will cultivate an AI system that replace much of the computing-intense MD simulations. Our current focus is heavily directed toward critical signaling proteins, including protein kinases and small G proteins, understanding their structural transformations that underlie their biological functions.

2. The "Swimming" Method & Complex Modeling

We develop methods centered around the "Swimming" method we pioneered to investigate molecular interactions at unprecedented granularity. This approach is instrumental in studying: * Protein-small molecule binding. * Protein-protein interactions. * Modeling the architectures of large, functional multiprotein complexes.

3. Computational Drug Discovery

We always aspire to translate the discoveries of our research into practical paths for drug discovery. We are particularly keen on tackling the so-called "undruggable" targets, providing novel structural insights to guide the design of next-generation therapeutics.

4. Wet-lab Experiments

It is an integral part of our lab, not an add-on. We consider all computational results hypotheses until we find convincing experimental support. We start devising experiments to test it the moment we have an idea, from simulations, AI or otherwise. We are always happy to change our ideas facing disagreeing evidence. We expect the experimental platform to expand rapidly in our lab in the near future.

A Note from the PI

Principal Investigator Dr. Yibing Shan. Against his training in physics he is fine with stamp-collecting style research. He enjoys even minute details of proteins. To his defense, if it brings about a drug, it's all worth it.