Centers & Labs

RIKEN Center for Life Science Technologies

Structural Bioinformatics Team

Team Leader: Kam Zhang (Ph.D.)
Kam  Zhang(Ph.D.)

The complex biological functions of proteins are determined by their equally intricate three-dimensional structures. The correctly folded native structure is critical for the proper function of a protein in a cell. Small deviations from its native structure can often lead to malfunction of the protein and cause diseases. Our goal is to understand and modulate protein functions through computational studies of their structures. We are developing methods for protein structure prediction and applying design principles to create proteins with novel architectures, new biological functions or effective therapeutics. We are exploring new avenues to solve the X-ray crystallographic phase problem. We are also developing and applying computational methods to discover new inhibitors for various drug targets.

Main Research Field

Multidisciplinary

Related Research Fields

Physics / Chemistry / Biology & Biochemistry / Computer Science

Research Subjects

  • Protein structure prediction and design
  • Ab initio phasing with de novo models
  • Virtual screening and drug design

Selected Publications

  1. Voet, A. R. D., Noguchi, H., Addy, C., Zhang, K. Y. J., Tame, J. R. H.:
    “Biomineralization of a Cadmium Chloride Nanocrystal by a Designed Symmetrical Protein.”
    Angew. Chem. Int. Ed., 54, 9857-9860. DOI:10.1002/anie.201503575. 2015
  2. Voet, A. R. D., Noguchi, H., Addy, C., Simoncini, D., Terada, D., Unzai, S., Park, S-Y., Zhang, K. Y. J., Tame, J. R. H.:
    “Computational design of a self-assembling symmetrical β-propeller protein.”
    Proc. Natl. Acad. Sci. U.S.A., 111, 15102-15107. 2014.
  3. Kumar, A., Ito, A., Hirohama, M., Yoshida, M., Zhang, K. Y. J.:
    “Identification of Sumoylation Inhibitors Targeting a Predicted Pocket in Ubc9.”
    J. Chem. Inf. Model., 54, 2784−2793. 2014.
  4. Voet, A.R.D., Ito, A., Hirohama, M., Matsuoka, S., Tochio, N., Kigawa, T., Yoshida, M., Zhang, K. Y. J.:
    “Discovery of small molecule inhibitors targeting the SUMO-SIM interaction using a protein interface consensus approach. 12.”
    Med. Chem. Commun., 5, 783-786. 2014.
  5. Kumar, A., Ito, A., Takemoto, M., Yoshida, M., Zhang, K. Y. J.:
    “Identification of 1, 2, 5-Oxadiazoles as a New Class of SENP2 Inhibitors Using Structure Based Virtual Screening.”
    J. Chem. Inf. Model., 54, 870–880. 2014
  6. Berenger, F., Voet, A., Lee, X.Y., Zhang, K. Y. J.:
    “A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening.”
    J. Cheminformatics, 6:23. 2014.
  7. Voet, A., Kumar, A., Berenger, F., Zhang, K. Y. J.:
    “Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4.”
    J. Comput-Aided Mol. Des., 28, 363-373. 2014.
  8. Shrestha, R., Zhang, K. Y. J.:
    “Improving fragment quality for de novo structure prediction.”
    Proteins: Struct., Funct., Bioinf., 82, 2240-2252. 2014.
  9. Simoncini, D., Zhang, K. Y. J.:
    “Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm.”
    PLoS ONE. 8 e68954. 2013.
  10. Berenger, F., Zhou, Y., Shrestha, R., Zhang, K. Y. J.:
    “Entropy-accelerated exact clustering of protein decoys.”
    Bioinformatics. 27 939. 2011.

Lab Members

Principal Investigator

Kam Zhang
Team Leader

Core Members

Ashutosh Kumar
Research Scientist
Pierre Thevenet
Postdoctoral Researcher
Daiki Terada
Junior Research Associate
Matej Janezic
International Program Associate
Rojan Shrestha
Visiting Scientist
David Simoncini
Visiting Scientist
Dileep Kalarickal Vijayan
Visiting Researcher
Aditya Padhi
Postdoctoral Researcher

Contact information

1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan
Tel: +81-(0)45-503-9560
Fax: +81-(0)45-503-9559

Email: kamzhang [at] riken.jp

Related links

Recent research results