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Welcome to my home page!

My name is Shuangye Yin. I am currently a postdoctoral researcher in Nikolay Dokholyan Group in Department of Biochemistry and Biophysics at University of North Carolina at Chapel Hill (UNC-CH). Although I received my background training in Physics (for B.S., M.S. and PhD degrees), my research area has been multidisciplinary, which includes nanowires, nano-clusters, protein modeling, drug design, and bioinformatics. The ever changing research fields is both interests driven as well as funding driven. The fun side of science is that you can always find something exciting as long as you dig deep enough.

My website is still under construction. Detailed explanation of some of the exciting research projects is on the way.

Research

Protein modeling

I paticipate in the developement of Medusa, a protein modeling and design suite written in C++. One of the application is to prediction protein stability change upon mutations. We have developed protocols to evaluation such stability changes. We collected a large set of ΔΔG experimental data and tested our protocol, and found remarkable correlation between our prediction and experimental measurments. The method is available freely through our web-based Eris server .

In addition, we find that modeling protein backbone flexiblity is essential for protein stability prediction, especially in cases when smaller buried residues are mutated to larger residues. In case when protein structure is not of high resolution, the flexible backbone methods can pre-relax the structure, and result in better ΔΔG prediction.

Drug design

Design of MedusaScore as a scoring function for virtual screening. Developement of MedusaDock as a flexible receptor and flexible ligand docking program.

Protein-protein interface design

Design novel protein-protein interaction interface. In one of the project, I use DMD to sample protein backbone conformation and develop protocols that can combine Rosetta to redesign a scaffold protein that will bind to PAK1. Due to the extra backbone sampling The new design has comparable binding affinity and is more stable.

Protein surface

I am also interest in fast comparison of protein surfaces. The new appraoch encode the 3D surfaces using geometric invariant descripts, which do not change under translation and rotation. Since comparison of fingerprints are fast, we are the first to perform a complete PDB screening for local surface patche similarities.

Publications

Book Chapters

Research Articles

Contacts

University of North Carolina at Chapel Hill
Department of Biochemistry and Biophysics
Genertic Medicine Building
120 Mason Farm Rd.
Chapel Hill, NC 27599
syin@email.unc.edu