| Name | LigandBox |
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| Aliases | LIGANDs Data Base Open and eXtensible |
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| 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. LigandBox has been developed by JBIC, as one component of the molecular simulation system myPresto, supported by NEDO. 3D conformations of compounds were generated from 2D structural data, kindly provided by Namiki Shoji Co.,Ltd. Compounds from Namiki Shoji Co.,Ltd can be ordered to each company through each inquiry web page. Chemical structures in this database were computationally generated, may not be identical to structures of compounds stored in supplying companies. |
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| Type | DB |
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| Main Institutes of management | Osaka University | National Institute of Advanced Industrial Science and Technology (AIST) |
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| Country of the Institute | Japan |
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| URL of the site | http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en | https://dbarchive.biosciencedbc.jp/en/ligandbox/desc.html |
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| Interface | GUI |
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| Input example | By entering the name of the small molecule compound, or entering the product number of the small molecule compound of Namiki Shoji Co.,Ltd. and Kishida Chemica Co.,Ltd., the three-letter of the small molecule compound of PDB, the KEGG_COMPOUND, the KEGG_DRUG, the ChEMBL_ID, or the PubChem_ID, you can search for compounds |
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| Keyword | Small molecule compound | 3D structure | MD simulation |
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| Amount of the all data for download（Mbyte） | Method to obtain the all data. | 27.7GB|http://www.mypresto5.com/ligandbox/cgi-bin/lbox_download.cgi?LANG=en |
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| External resources (databases) in building the product. | PDB |
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| Data type | Small molecule structure |
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| Biological species in the main concern | None |
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| Conditions of use | None |
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| Frequency of updates (in last two years) | any time |
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| Last date of updates (date of confirmation) | 2018/08/13 (2021/12/09) |
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| Main IDs used in the products | PDBID | KEGG_ID | PubChem_ID | ChEMBL_ID | SMILES |
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| How to make a link to get access to each IDs. | http://www.mypresto5.com/ligandbox/cgi-bin/lbox_propsch_input.cgi?LANG=en | http://www.mypresto5.com/ligandbox/cgi-bin/lbox_strsch_input.cgi?LANG=en |
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| external databases to which this database/tool have links | PDB |
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| Published papers (PubMed IDs) | pmid:27493549 |
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| Operational Status | available |
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