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Welcome to my home page! I recently moved to Broad Institute as a staff scientist working on computational research and development in the Genome Sequencing and Analysis program.

During 2006 to 2010, I was 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 has been multidisciplinary, which includes nanowires, nanoclusters, protein modeling, protein design, and drug design. The ever changing research fields is both curiosity driven and funding driven. The fun side of science is that you can always find something interesting as long as you dig deep enough.

Research

Protein modeling & design

I participate in the development 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 measurements. The method is available freely through our web-based Eris server .

In addition, we find that modeling protein backbone flexibility 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. Development 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 approach encode the 3D surfaces using geometric invariant descriptors, 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 patch similarities.

Publications

Book Chapters

Research Articles ( The list and citation in ResearcherID)

Contacts

Broad Institute
Genome Sequencing and Analysis Program
320 Charles St, Rm 2244
Cambridge, MA 02141
shuangye AT broadinstitute.org
syin AT email.unc.edu