BDR researchers coming from diverse research fields are working together to achieve higher goals.

Seminars & Symposia

Seminars & Symposia

BDR hosts annual symposium and regular seminars inviting international scientists in life science.

Careers & Study

Careers & Study

BDR embraces people from diverse backgrounds, and strives to create an open and supportive setting for research.



BDR communicates the appeal and significance of our research to society through the use of various media and activities.



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About Us

About Us

Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Photo of Team leder, Teruki Honma

Team Leader
Teruki Honma Ph.D.

Laboratory for Structure-Based Molecular Design

Location Yokohama


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New in silico molecular design technologies are developed and applied to drug discovery targets

Through the long history of small molecule drug discovery, conventional “druggable” targets had been already investigated and many drugs were marketed. On the other hand, in addition to refractory cancer, Alzheimer's disease, genetic diseases, the risk of new infections is increasing, so there are strong needs for innovative new drugs that have never existed. The team develops new technologies for in silico design and drug discovery artificial intelligence (AI) by combining simulation such as molecular dynamics and quantum chemical calculation (FMO method) and informatics technology represented by AI. The developed technologies are applied to in silico screening for drug discovery targets with high difficulty by conventional. Using the hits obtained by the screening, simultaneous optimization of multiple items necessary for medicines such as potency, pharmacokinetics, toxicity etc. is carried out. In addition, we develop and operate the world's first quantum chemistry calculation database (FMO IFIE database) of proteins.

Research Theme

  • Development of new technologies for in silico drug discovery combining simulation and informatics
  • Application of in silico drug discovery technologies to drug discovery targets
  • Construction and publication of FMO IFIE database

Selected Publications

Komura H, Watanabe R, Kawashima H, et al.
A public-private partnership to enrich the development of in silico predictive models for pharmacokinetic and cardiotoxic properties.
Drug discovery today 26(5), 1275-1283 (2021) doi: 10.1016/j.drudis.2021.01.024

Sato T, Hashimoto N, Honma T.
Bioisostere Identification by Determining the Amino Acid Binding Preferences of Common Chemical Fragments.
Journal of Chemical Information and Modeling 57(12), 2938-2947 (2017) doi: 10.1021/acs.jcim.7b00092

Watanabe C, Watanabe H, Fukuzawa K, et al.
Theoretical Analysis of Activity Cliffs among Benzofuranone Class Pim1 Inhibitors Using the Fragment Molecular Orbital Method with Molecular Mechanics Poisson-Boltzmann Surface Area (FMO+MM-PBSA) Approach.
Journal of Chemical Information and Modeling 57(12), 2996-3010 (2017) doi: 10.1021/acs.jcim.7b00110

Okada-Iwabu M, Yamauchi T, Iwabu M, et al.
A small-molecule AdipoR agonist for type 2 diabetes and short life in obesity.
Nature 503, 493-499 (2013) doi: 10.1038/nature12656

Saito Y, Yuki H, Kuratani M, et al.
A pyrrolo-pyrimidine derivative targets human primary AML stem cells in Vivo..
Science Translational Medicine 5(181), 181ra152 (2013) doi: 10.1126/scitranslmed.3004387

Shiba T, Kido Y, Sakamoto K, et al.
Structure of the trypanosome cyanide-insensitive alternative oxidase.
Proceedings of the National Academy of Sciences of the United States of America 110(12), 4580-5 (2013) doi: 10.1073/pnas.1218386110

Takaya D, Sato T, Yuki H, et al.
Prediction of Ligand-Induced Structural Polymorphism of Receptor Interaction Sites Using Machine Learning.
Journal of Chemical Information and Modeling 53(3), 704-716 (2013) doi: 10.1021/ci300458g

Sato T, Watanabe H, Tsuganezawa K, et al.
Identification of novel drug-resistant EGFR mutant inhibitors by in silico screening using comprehensive assessments of protein structures.
Bioorganic & Medicinal Chemistry 20(12), 3756-67 (2012) doi: 10.1016/j.bmc.2012.04.042

Yuki H, Honma T, Hata M, Hoshino T.
Prediction of sites of metabolism in a substrate molecule, instanced by carbamazepine oxidation by CYP3A4.
Bioorganic & Medicinal Chemistry 20(2), 775-83 (2011) doi: 10.1016/j.bmc.2011.12.004

Sato T, Honma T, Yokoyama S.
Combining Machine Learning and Pharmacophore-based Interaction Fingerprint for in silico Screening.
Journal of Chemical Information and Modeling 50(1), 170-85 (2010) doi: 10.1021/ci900382e

Sato T, Matsuo Y, Honma T, Yokoyama S.
In silico functional profiling of small molecules and its applications.
Journal of Medicinal Chemistry 51(24), 7705-16 (2008) doi: 10.1021/jm800504q


Teruki Honma

Team Leader

Masateru Ota

Senior Scientist

Kazuyoshi Ikeda

Senior Scientist

Chie Takemoto

Research Scientist

Hitomi Yuki

Technical Scientist

Tomohiro Sato

Research Scientist

Chiduru Watanabe

Research Scientist

Kikuko Kamisaka

Technical Scientist

Mayuko Yasuda

Expert Technician

Norihiko Tani

Technical Staff I

Yuki Saito


Hiroshi Iijima

Senior Visiting Scientist

Daisuke Takaya

Visiting Scientist