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Assistant Professor (also with Biochemistry and Molecular Biology); Ph.D., University of Illinois at Chicago, 2006
Research Description 
Protein structure, function, classification and evolution;
Disease-associated non-synonymous single-nucleotide polymorphism;
Geometric matching techniques;
Geometric modeling and molecular simulation
Areas of ResearchComputational Structural Biology
Molecular Structural Evolution
Bioinformatics
Research Interests
In our lab, we study protein structure, function, classification and evolution. We use geometric approaches to address biological and medical issues of protein and RNA structures in Structural Biology and Molecular Evolution. We design parallel algorithms to perform large-scale computations on these 3D structures via Beowulf Linux clusters.
Our research focuses on protein structure and function by using protein shape analysis. We are also interested in the areas of surface identification, characterization, and classification, geometric and evolutionary matching techniques, disease-associated non-synonymous single-nucleotide polymorphism (nsSNP), structural variations associated with gene duplication and Knot theory applied in RNA structures. Novel areas of research include the use of high-throughout computing technology for generating millions of surface patches to study protein-protein interactions and geometric modeling for drug discovery.
In practice, we have developed geometric methods and constructed web-based databases and servers:
SplitPocket, for studying protein functional surfaces,
fPOP, for surface comparisons, and residue matching profiling,
PSD, for predicting protein binding site residues from sequences and,
PSC, for constructing protein surface classification. The developed methods allow us to obtain theoretical results from high-throughput computations to identify spatially constrained residues of importance and to predict the protein binding surfaces from primary sequences by the templates of spatial patterns. From these studies, we aim to derive fundamental principles of molecular structure and hope to have a biological impact on biomedicine for facilitating the discovery and development of therapeutic drugs. Lab website at
http://pocket.uchicago.edu/ytseng/.
Selected Publications1. Tseng YY, Li WH. PSC: protein surface classification. Nucleic Acids Res 40: W435-9. 2012.
2. Tseng YY, Li WH. Classification of protein functional surfaces using structural
characteristics. Proc Natl Acad Sci U S A 109(4): 1170-5, 2012.
3. Tseng YY, Li WH. Evolutionary approach to predicting the binding site residues of a
protein from its primary sequence. Proc Natl Acad Sci U S A 108(13): 5313-8, 2011.
4. Tseng YY, Chen ZJ, Li WH. fPOP: footprinting functional pockets of proteins by
comparative spatial patterns. Nucleic Acids Res 38: D288-95, 2010.
5. Tseng YY, Dupree C, Chen ZJ, Li WH. SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns. Nucleic Acids Res 37: W384-9, 2009.
6. Tseng YY, Li WH. Identification of protein functional surfaces by the concept of a split pocket. Proteins 76(4): 959-76, 2009.
7. Tseng YY, Dundas J, Liang J. Predicting protein function and binding profile via matching of local evolutionary and geometric surface patterns. J Mol Biol 387(2): 451-64, 2009.
8. Adamian L, Gussin HA, Tseng YY, Muni NJ, Feng F, Qian H, Pepperberg DR, Liang J. Structural model of rho1 GABA(C) receptor based on evolutionary analysis: Testing of
predicted protein-protein interactions involved in receptor assembly and function.
Protein Sci, 2009.
9. Tseng YY, Liang J. Predicting enzyme functional surfaces and locating key residues
automatically from structures. Ann Biomed Eng 35(6): 1037-42, 2007.
10. Tseng YY, Liang J. Estimation of amino acid residue substitution rates at local spatial
regions and application in protein function inference: a Bayesian Monte Carlo approach.
Mol Biol Evol 23(2): 421-36, 2006.
11. Adamian L, Ouyang Z, Tseng YY, Liang J. Evolutionary patterns of retinal-binding pockets of type I rhodopsins and their functions. Photochem Photobiol 82(6): 1426-35, 2006.
12. Dundas J, Ouyang Z, Tseng YY, Binkowski A, Turpaz Y, Liang J. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of
functionally annotated residues. Nucleic Acids Res 34: W116-8, 2006.
13. Tseng YY, Liang J. Are residues in a protein folding nucleus evolutionarily conserved? J Mol Biol 335(4): 869-80, 2004.
14. Stitziel NO, Binkowski TA, Tseng YY, Kasif S, Liang J. topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res 32: D520-2, 2004.
15. Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, Liang J. Structural location of disease-associated single-nucleotide polymorphisms. J Mol Biol 327(5): 1021-30, 2003.
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