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.
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
Design of MedusaScore as a scoring function for virtual screening.
Development of MedusaDock as a flexible receptor and flexible ligand docking
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.
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
- S. Yin, F. Ding, and N. V. Dokholyan, "Computational evaluation of protein stability change upon mutations using Eris.", in "In Vitro Mutagenesis Protocols" Editor: J. Braman. Humana Press (2010)
- S. Yin, F. Ding, and N. V. Dokholyan, "Modeling Mutations in Proteins Using Medusa and Discrete Molecule Dynamics.", in "Protein Structure Prediction: Method and Algorithms" Editor: H. Rangwala and G. Karypis, Wiley & Sons (in press)
S. Yin and N. V. Dokholyan, "Fingerprint-Based Structure Retrieval Using Electron Density", PROTEINS: Structure, Function, and Bioinformatics, (in press)
F. Ding, S. Yin, and N. V. Dokholyan, "Rapid flexible docking using a stochastic rotamer library of ligands", Journal of Chemical Information and Modeling, 50, 1612-1632 (2010)
R. K. Jha, A. Leaver-Fay, S. Yin, Y. Wu, G. Butterfoss, T. Szyperski, N. V. Dokholyan, and B. Kuhlman, "Computational design of a PAK1 binding protein", Journal of Molecular Biology , 400, 257-270 (2010)
- J. Bowlan, C. N. van Dijk, A. Kirilyuk, A. Liang, S. Yin, T. Rasing, and W. A. de Heer "Size dependent magnetic moments and electric polarizabilities of free Tb, Ho, and Tm clusters ", Journal of Applied Physics , 107:09B509 (2010)
- S. Yin, E. A. Proctor, A. A. Lugovskoy, and N. V. Dokholyan, "Fast screening of protein surfaces using geometric invariant fingerprints", Proceedings of the National Academy of Sciences USA, 106:16622-16626 (2009)
- S. Yin, L. Biedermannova, J Vondrasek, and N. V. Dokholyan, "MedusaScore: An Accurate Force-Field Based Scoring Function for Virtual Drug Screening", Journal of Chemical Information and Modeling, 48:1656-1662 (2008)
- Y. Chen, F. Ding, H. Nie, A. W. Serohijos, S. Sharma, K. C. Wilcox, S. Yin, and N. V. Dokholyan, "Protein folding: then and now", Archives of Biochemistry and Biophysics, 469:4-19 (2008)
- S. Yin, F. Ding, and N. V. Dokholyan, "Modeling backbone flexibility improves protein stability estimation", Structure, 15:1567-1576 (2007)
- S. Yin, F. Ding, and N. V. Dokholyan, "Eris: An automated estimator of protein stability", Nature Methods, 4:466-467 (2007)
- S. Yin, X. Xu, A. Liang, J. Bowlan, R. Moro, and W. A. de Heer, "Electron pairing in ferroelectric niobium and niobium alloy clusters", Journal of Superconductivity and Novel Magnetism, 21:265-269 (2008).
- X. Xu, S. Yin, R. Moro, and W. A. de Heer, "Distribution of magnetization of a cold ferromagnetic cluster beam", Physical Review B, 78:054430 (2008)
- S. Yin, R. Moro, X. S. Xu, and W. A. de Heer, "Magnetic enhancement in cobalt-manganese alloy clusters", Physical Review Letters, 98:113401 (2007)
- X. S. Xu, S. Yin, R. Moro, A. Liang, J. Bowlan, and W. A. de Heer, "Nonclassical dipoles in cold niobium clusters", Physical Review B, 75:085429 (2007)
- S. Yin, X. S. Xu, R. Moro, and W. A. de Heer, "Measurement of magnetic moments of free BiNMnM clusters", Physical Review B, 72:174410 (2005)
- X. S. Xu, S. Yin and W. A. de Heer, "Magnetic moments and adiabatic magnetization of free cobalt clusters", Physical Review Letters, 95:237209 (2005)
- R. Moro, S. Yin, X.S. Xu, and W.A. de Heer, "Spin uncoupling in free Nb clusters: Support for nascent superconductivity", Physical Review Letters, 93:086803 (2004)
- R. Moro, X.S. Xu, S. Yin, and W.A. de Heer, "Ferroelectricity in free niobium clusters", Science, 300:1265-1269 (2003)
- B.L. Wang, S. Yin, G.H. Wang, and J.J. Zhao, "Structures and electronic properties of ultrathin titanium nanowires", Journal of Physics-Condensed Matter, 13:L403-L408 (2001)
- B.L. Wang, S. Yin, G.H. Wang, A. Buldum, and J.J. Zhao, "Novel structures and properties of gold nanowires", Physical Review Letters, 86:2046-2049 (2001)
- T.X. Li, S. Yin, Y.L. Ji, B.L. Wang, G.H. Wang, and J.J. Zhao, "A genetic algorithm study on the most stable disordered and ordered configurations of Au38-55", Physics Letters A, 267:403-407 (2000)
- S.W. Yu, G.H. Wang, S. Yin, Y.X. Zhang, and Z.G. Liu, "Nanostructured films of boron suboxide by pulsed laser deposition", Physics Letters A, 268:442-447 (2000).
Genome Sequencing and Analysis Program
320 Charles St, Rm 2244
Cambridge, MA 02141
shuangye AT broadinstitute.org
Please note that I cannot access emails sent to syin AT email.unc.edu anymore.