| URL: | http://ligandbox.protein.osaka-u.ac.jp/ligandbox |
| Full name: | A database for 3D structures of chemical compounds |
| Description: | LigandBox(LIGANDs Data Base Open and eXtensible) is a 'ready-to-dock' database of small chemical compounds, for virtual drug screening on computer docking studies. It contains the 3D molecular structures including full hydrogen atoms with atomic charges for each compounds. |
| Year founded: | 2013 |
| Last update: | 20170927 |
| Version: | 201610_2 |
| Accessibility: |
Accessible
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| Country/Region: | Japan |
| Data type: | |
| Data object: |
NA
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| Database category: | |
| Major species: |
NA
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| Keywords: |
| University/Institution: | Osaka University |
| Address: | |
| City: | Osaka |
| Province/State: | |
| Country/Region: | Japan |
| Contact name (PI/Team): | Takeshi Kawabata |
| Contact email (PI/Helpdesk): | kawabata@protein.osaka-u.ac.jp |
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LigandBox: A database for 3D structures of chemical compounds. [PMID: 27493549]
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. |