Team Leader
Kam Zhang Ph.D.

Laboratory for Structural Bioinformatics

[Closed Mar. 2023]

E-mailkamzhang[at]riken.jp

Please replace [at] with @.

We compute for life.

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

Selected Publications

Alfi A, Popov A, Kumar A, et al.
Cell-Free Mutant Analysis Combined with Structure Prediction of a Lasso Peptide Biosynthetic Protease B2.
ACS Synthetic Biology 11(6), 2022-2028 (2022) doi: 10.1021/acssynbio.2c00176

Yagi S, Padhi AK, Vucinic J, et al.
Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase.
Journal of the American Chemical Society (2021) doi: 10.1021/jacs.1c05367

Kaushik R, Zhang KYJ.
ProFitFun: A Protein Tertiary Structure Fitness Function for Quantifying the Accuracies of Model Structures.
Bioinformatics (Oxford, England) (2021) doi: 10.1093/bioinformatics/btab666

Padhi AK, Kumar A, Haruna KI, et al.
An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes.
Briefings in bioinformatics (2021) doi: 10.1093/bib/bbab338

Jiang X, Kumar A, Motomura Y, et al.
A Series of Compounds Bearing a Dipyrido-Pyrimidine Scaffold Acting as Novel Human and Insect Pest Chitinase Inhibitors.
Journal of medicinal chemistry 63(3), 987-1001 (2020) doi: 10.1021/acs.jmedchem.9b01154

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

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

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