著者

Takeshi Kawabata Yusuke Sugihara Yoshifumi Fukunishi Haruki Nakamura

出版者

日本生物物理学会

雑誌

BIOPHYSICS (ISSN:13492942)

巻号頁・発行日

vol.9, pp.113-121, 2013 (Released:2013-08-07)

参考文献数

30

被引用文献数

8 25

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A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

著者

Haruki Nakamura

出版者

The Biophysical Society of Japan

雑誌

Biophysics and Physicobiology (ISSN:21894779)

巻号頁・発行日

vol.20, no.4, pp.e200040, 2023 (Released:2023-11-07)

参考文献数

8

著者

Junko Sato Kouji Kozaki Susumu Handa Takashi Ikeda Ryotaro Saka Kohei Tomizuka Yugo Nishiyama Toshiyuki Okumura Shinichi Hirai Tadashi Ohno Mamoru Ohta Susumu Date Haruki Nakamura

出版者

一般社団法人 情報処理学会

雑誌

IPSJ Transactions on Bioinformatics (ISSN:18826679)

巻号頁・発行日

vol.6, pp.9-17, 2013 (Released:2013-05-28)

参考文献数

13

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We developed a new information management system, Protein Experimental Information Management System (PREIMS), which has the ontology-based functions for quality control, validation, scalability, and information sharing. Its contents are mainly experimental protocols for the analyses of protein structures and functions, and their results. They are stored separately in the PREIMS database (DB), as the ontology based protocol data and the result data. The synchrotron experimental information was stored as the latter result data in Extensible Markup Language (XML). Furthermore we converted those protocols in the format of Resource Description Framework (RDF) for integration with other biological information resources.

著者

Haruki Nakamura

出版者

The Biophysical Society of Japan

雑誌

Biophysics and Physicobiology (ISSN:21894779)

巻号頁・発行日

pp.bppb-v18.035, (Released:2021-12-02)

著者

Haruki Nakamura Masahide Kikkawa Takeshi Murata

出版者

The Biophysical Society of Japan

雑誌

Biophysics and Physicobiology (ISSN:21894779)

巻号頁・発行日

pp.bppb-v18.030, (Released:2021-10-23)

著者

Kota Kasahara Hiroki Terazawa Hayato Itaya Satoshi Goto Haruki Nakamura Takuya Takahashi Junichi Higo

出版者

The Biophysical Society of Japan

雑誌

Biophysics and Physicobiology (ISSN:21894779)

巻号頁・発行日

pp.BSJ-2020013, (Released:2020-10-15)

被引用文献数

9