Laboratory for Structural Bioinformatics | RIKEN BDR

Laboratory for Structural Bioinformatics

Team Leader

Kam ZhangPh.D.

We compute for life.

Research Summary

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 developing new methods of model building and refinement for X-ray and Cryo-EM. We are also developing and applying computational methods to discover new inhibitors for various drug targets.

Research Theme

  • Protein structure prediction and design
  • X-ray and Cryo-EM model building and refinement
  • Virtual screening and drug design

Main Publications List

  • Kumar A, Zhang KYJ
    A cross docking pipeline for improving pose prediction and virtual screening performance.
    Journal of Computer-Aided Molecular Design 32. 163-173 (2018) doi:10.1007/s10822-017-0048-z.
  • Terada D, Voet ARD, Noguchi H, et al.
    Computational design of a symmetrical ß-trefoil lectin with cancer cell binding activity.
    Scientific Reports 7. 5943 (2017) doi:10.1038/s41598-017-06332-7.
  • 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.
  • 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.
  • 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.
  • 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 America 111. 15102-15107 (2014) doi: 10.1073/pnas.1412768111
  • 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
  • Kumar A, Ito A, Takemoto M, et al.
    Identification of 1,2,5-Oxadiazoles as a New Class of SENP2 Inhibitors Using Structure Based Virtual Screening.
    Journal of Chemical Information and Modeling 54. 870–880 (2014) doi: 10.1021/ci4007134
  • 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
  • Berenger F, Zhou Y, Shrestha R, Zhang KYJ.
    Entropy-accelerated exact clustering of protein decoys.
    Bioinformatics 27. 939 (2011) doi: 10.1093/bioinformatics/btr072

Member

Kam ZhangTeam Leader kamzhang[at]riken.jp
Ashutosh KumarSenior Scientist akumar[at]riken.jp
Aditya PadhiPostdoctoral Researcher adityakumar.padhi[at]riken.jp
Kutumbarao NidamarthiResearch Scientist h.nidamarthi[at]riken.jp
Dileep Kalarickal VijayanVisiting Researcher dileep.kalarickalvijayan[at]riken.jp
Matej JanezicInternational Program Associate matej.janezic[at]riken.jp
Erma MuhammadInternational Program Associate ermafatiha.muhammad[at]riken.jp
David SimonciniVisiting Scientist
Rojan ShresthaVisiting Scientist
Francois BerengerVisiting Scientist

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