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RIKEN Center for Biosystems Dynamics Research Laboratory for Structural Bioinformatics

Team Leader: Kam Zhang (Ph.D.)

Research Summary

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 Fields

  • 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. Jiang X., Kumar A., Motomura Y., et al.:
    "A series of compounds bearing a dipyrido-pyrimidine scaffold acting as novel human and insect pest chitinases inhibitors."
    Journal of Medicinal Chemistry 63, 987-1001 (2020). doi:10.1021/acs.jmedchem.9b01154.
  • 2. Kumar A., Zhang KYJ.:
    "Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model."
    Journal of Computer-Aided Molecular Design 33, 1045-1055 (2019). doi:10.1007/s10822-019-00220-0.
  • 3. Terada D, Voet ARD, Noguchi H, et al.:
    "Computational design of a symmetrical s-trefoil lectin with cancer cell binding activity."
    Scientific Reports 7. 5943 (2017) doi:10.1038/s41598-017-06332-7.
  • 4. Matsuoka M, Kumar A, Muddassar M, et al.:
    "Discovery of Fungal Denitrification Inhibitors by Targeting Copper Nitrite Reductase from Fusarium Oxysporum."
    Journal of Chemical Information and Modeling 57. 203-213 (2017) doi:10.1021/acs.jcim.6b00649.
  • 5. Kumar A, Zhang KYJ.:
    "A pose prediction approach based on ligand 3D shape similarity."
    Journal of Computer-Aided Molecular Design 30. 457-469 (2016) doi:10.1007/s10822-016-9923-2.
  • 6. Voet ARD, Noguchi H, Addy C, et al.:
    "Biomineralization of a Cadmium Chloride Nanocrystal by a Designed Symmetrical Protein."
    Angewandte Chemie International Edition 54. 9857-9860 (2015) doi:10.1002/anie.201503575.
  • 7. Kumar A, Ito A, Hirohama M, et al.:
    "Identification of Sumoylation Inhibitors Targeting a Predicted Pocket in Ubc9."
    Journal of Chemical Information and Modeling 54. 2784?2793 (2014) doi: 10.1021/ci5004015
  • 8. Voet ARD, Noguchi H, Addy C, et al.:
    "Computational design of a self-assembling symmetrical β-propeller protein."
    Proceedings of the National Academy of Sciences of United States of America111. 15102-15107 (2014) doi: 10.1073/pnas.1412768111
  • 9. Simoncini D, Zhang KYJ.:
    "Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm."
    PLoS ONE 8. e68954 (2013) doi: 10.1371/journal.pone.0068954
  • 10. Berenger F, Zhou Y, Shrestha R, Zhang KYJ.:
    "Entropy-accelerated exact clustering of protein decoys."
    Bioinformatics 27. 939-945 (2011) doi: 10.1093/bioinformatics/btr072

Related Links

Lab Members

Principal investigator

Kam Zhang
Team Leader

Core members

Ashutosh Kumar
Senior Scientist
Dileep Kalarickal Vijayan
Research Scientist
Rahul Kaushik
Research Scientist
Kutumbarao Nidamarthi
Research Scientist
Aditya Padhi
Visiting Researcher
Erma Fatiha Binti Muhammad
International Program Associate
Chun Lai Tam
International Program Associate
Matej Janezic
Student Trainee
Francois Berenger
Visiting Scientist
Rojan Shrestha
Visiting Scientist
David Simoncini
Visiting Scientist

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

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