Welcome!

Welcome to Yu Lab! We are studying biophysical(computational and experimental) approaches of proteins and Computational Neuroscience.

Research

Protein Folding

Finding out folding pathways
  • Folding pathway study
  • Folding cooperativity
  • Protein Structure
More detail


Hydrogen Exchange (HX)

with amino acid resolution
  • Denaturant dependent HX
  • Building folding pathway
  • Site-resolved HDX-MS
More detail


Computational Neuroscience

Modeling/Simulation using computer
  • Neural networks
  • Neural encoding
  • Modeling
More detail

Protein Dynamics

And conformational change
  • Moleculary Dynamics simulation
  • Monte Carlo Simulation
  • Hydrogen Exchange
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Simulation versus Experiment

Comparison with Sim. & Exp.
  • MD versus HX-NMR
  • MD versus HDX-MS
  • Simulation versus Experiment
More detail


Protein Structure Prediction

From amino acid sequence
  • Secondary Structure Prediction
  • Tertiary Structure Prediction
  • Contact Prediction
More detail

Protein Protein Interaction

How protein bind?
  • Hydrogen Exchange
  • MD simulation
  • Protein Docking
More detail


Protein Structure Study

From coevolutionary information
  • Statistical Coupling Analysis
  • Direct Coupling Analysis
  • Neurodegenerative proteins
More detail


Others

For other biological problems
  • Proteomics
  • Big data analysis
  • Computational Biology
More detail





MEMBERS

Principal Investigator





PUBLICATIONS

  • Zachary Gates, Michael C Baxa, Wookyung Yu, Joshua A Riback, Hui Li, Benoit Roux , Stephen Kent and Tobin R Sosnick
    The perplexing cooperative folding and stability of a low sequence complexity, poly-proline 2 protein lacking a hydrophobic core. (Under Review, PNAS)

  • Wookyung Yu, Michael C. Baxa, Isabelle Gagnon, Karl F. Freed and Tobin R. Sosnick
    Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange
    Proceeding of The National Academy of Science USA, 113, 4747 (2016) (First Author)

  • Michael C. Baxa, Wookyung Yu, Aashish N. Adhikari, Liang Ge, Zhen Xia, Ruhong Zhou, Karl F. Freed and Tobin R. Sosnick
    Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar
    Proceeding of The National Academy of Science USA, 112, 8302 (2015) (Co-Author)

  • John J. Skinner&, Wookyung Yu&, Elizabeth K. Gichana, Michael C. Baxa, James Hinshaw, Karl F Freed, Tobin R. Sosnick, (&Co-first author.)
    Benchmarking all-atom simulations using hydrogen exchange.
    Proceeding of The National Academy of Science USA, 111, 15975 (2014) (Co-first Author)

  • Woonghee Lee, Wookyung Yu, Sukhmann Kim, Iksoo Chang, Weontae Lee,
    John L. Markley PACSY, a relational database management system for protein structure and chemical shift analysis.
    Journal of Biomolecular NMR, 54, 169 (2012) (Co-Author)

  • Wookyung Yu, Woonghee Lee, Weontae Lee, Sukhmann Kim and Iksoo Chang
    Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids.
    Journal of Biomolecular NMR, 51, 411 (2011) (First Author)

  • Yongbin Xu, Saemee Song, Arne Moeller, Nahee Kim, Shunfu Piao, Se-Hoon Sim, Mooseok Kang, Wookyung Yu, Hyun-Soo Cho, Iksoo Chang, Kangseok Lee, Nam-Chul Ha
    Functional implications of an intermeshing cogwheel-like interaction between TolC and MacA in the action of macrolide-specific efflux pump MacAB-TolC.
    Journal of Biological Chemistry 286, 13541 (2011) (Co-Author)

  • Wookyung Yu, and Iksoo Chang
    Identification of critical amino acids' interaction network affecting protein stability based on the Laplacian network analysis,
    Sae Mulli (New Physics) 61, 931 (2011) (First Author)

  • Wookyung Yu, Kwanghoon Chung, Mookyung Cheon, Muyoung Heo, Kyou-Hoon Han, Sihyun Ham and Iksoo Chang
    Cooperative folding kinetics of BBL protein and peripheral subunit-binding domain homologues
    Proceeding of The National Academy of Science USA, 105, 2397 (2008) (First Author)

  • Mookyung Cheon, Eunjoung Moon, Wookyung Yu, Choongrak Kim and Iksoo Chang
    Identifying the biological and physical essence of protein-protein network for yeast proteome ; Eigenvalue and perturbation analysis of Laplacian matrixs
    Sae Mulli (New Physics) 55, 47 (2007) (Co-Author)

   2016

   2016

Contact

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Contact

Wookyung Yu

Department of Brain & Cognitive Science
Daegu Gyeongbuk Institute of Science and Technology
Office: E4-514
Email: wkyu@dgist.ac.kr
Tel: +82-53-785-6152