RIKEN Center for Life Science Technologies


  • Research

    Latest publications from CLST.
  • News

    Awards, agreements, and other news.
  • Events

    Upcoming and past events including seminars, symposiums, open days.

For Public

To let you know about our research, this area contains 4 types of information about CLST; “Article”, “Videos”, “Event” and “Study”.
At “Article”, you can read articles on interviews and lectures, and you can enjoy the videos about CLST at “Videos”. If you want to meet and talk directly with the researcher, “Visit” give you some information of such events. You can find more difficult contents to know about our research deeply at “Study”.
  • Article
  • Event
  • Videos
  • Study

Labs & Technologies

Structural Bioinformatics Team

We compute for life.


* Due to the reorganization starting as new centers in April 2018, this laboratory is now belong to the Center for Biosystems Dynamics Research. As for the latest information, please see the following URL below.
> The webpage of Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research

Team Leader
Kam Zhang  Ph.D.

1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
Tel: 045-503-9560


>>> Lab Site

Research Area

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 Publications List


Biomineralization of a Cadmium Chloride Nanocrystal by a Designed Symmetrical Protein.

Voet AR, Noguchi H, Addy C, Zhang KYJ, Tame JR.
Angew Chem Int Ed Engl., 54(34), 9857-9860 (2015).

Computational design of a self-assembling symmetrical β-propeller protein

Voet AR, Noguchi H, Addy C, Simoncini D, Terada D, Unzai S, Park SY, Zhang KYJ, Tame JR.
Proc Natl Acad Sci USA, 111(42), 15102-15107 (2014).

Identification of sumoylation inhibitors targeting a predicted pocket in Ubc9

Kumar A, Ito A, Hirohama M, Yoshida M, Zhang KYJ.
J Chem Inf Model, 54, 2784-2793 (2014).

Discovery of small molecule inhibitors targeting the SUMO–SIM interaction using a protein interface consensus approach

Voet ARD, Ito A, Hirohama M, Matsuoka S, Tochio N, Kigawa T, Yoshida M, Zhang KYJ.
Med Chem Commun, 5(6), 783-786 (2014).

Identification of 1,2,5-oxadiazoles as a new class of SENP2 inhibitors using structure based virtual screening.

Kumar A, Ito A, Takemoto M, Yoshida M, Zhang KYJ.
J Chem Inf Model, 54(3), 870-880 (2014).

A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening

Berenger F, Voet A, Lee XY, Zhang KYJ.
Journal of Cheminformatics, 6(23), (2014).

Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4

Voet AR, Kumar A, Berenger F, Zhang KYJ.
J Comput Aided Mol Des, 28(4), 363-373 (2014).

Improving fragment quality for de novo structure prediction

Shrestha R, Zhang KYJ.
Proteins, 82(9), 2240-2252 (2013).

Entropy-accelerated exact clustering of protein decoys.

Berenger F, Zhou Y, Shrestha R, Zhang KYJ.
Bioinformatics, 27(7), 939-945 (2011).

>>>ALL Publications

Member  *concurrent

CLST was reorganized into three centers according to the RIKEN 4th Medium-Term Plan from April 1, 2018. For the latest information of Structural Bioinformatics Team, please visit the following websites.

> The webpage of Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research [http://www.bdr.riken.jp/en/research/labs/zhang-k/index.html]