Database Description

General information of database

Database name

LigandBox

Alternative name

LIGANDs Data Base Open and eXtensible

DOI

10.18908/lsdba.nbdc00551-000.V004

Version

V4	10.18908/lsdba.nbdc00551-000.V004	Update History
V3	10.18908/lsdba.nbdc00551-000.V003	Update History
V2	10.18908/lsdba.nbdc00551-000.V002	Update History
V1	10.18908/lsdba.nbdc00551-000.V001	-

Creator

Creator Name:

Yoshifumi Fukunishi*

Creator Affiliation:

Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST)

Journal Search:

Creator Name:

Takeshi Kawabata

Creator Affiliation:

Institute for Protein Research, Osaka University

Journal Search:

Creator Name:

Yusuke Sugihara

Creator Affiliation:

Fujitsu Kyushu Systems, Ltd

Creator Name:

Kohta Sakai

Creator Affiliation:

Fujitsu Kyushu Systems, Ltd

Journal Search:

Creator Name:

Hiroshi Kusudo

Creator Affiliation:

Hitachi Solutions East Japan, Ltd.

Journal Search:

Creator Name:

Yoshiaki Mikami

Creator Affiliation:

Hitachi Solutions East Japan, Ltd.

Journal Search:

Creator Name:

Tadaaki Mashimo

Creator Affiliation:

IMSBIO Co., Ltd

Journal Search:

Creator Name:

Haruki Nakamura

Creator Affiliation:

Institute for Protein Research, Osaka University

Journal Search:

Contact address

https://www.mypresto5.jp/contact/

Database classification

Structure Databases - Small molecules

Database 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.

Features and manner of utilization of database

The molecular files are in Sybyl mol2 file format for virtual drug screening, protein-compound docking, and chemo-informatics.The partial atomic charges of each compound is calculated by MOPAC AM1-BCC and the users can adopt these charges in the molecular dynamics simulations.Each compound has physical properties such as solubility and partition coefficient. These information is useful to avoid promiscuous compounds.The compound IDs are the vender’s ID to purchase the compounds and the inventory ratio is high.

License

Background and funding

The following projects of Japan Biological Informatics Consortium (JBIC):
- Structural Proteomics Project (https://togodb.biosciencedbc.jp/entry/lsdb_project_en/11)
- Development of Basic Technology for Protein Structure Analysis Aimed at Acceleration of Drug Discovery Research (https://togodb.biosciencedbc.jp/entry/lsdb_project_en/10)
- Development of Innovative Drug Discovery Platform Utilizing Information Technology(http://www.jbic.or.jp/english/rd/004.html )

Support by New Energy and Industrial Technology Development Organization (NEDO) and Ministry of Economy, Trade and Industry (METI)The following projects of Technology Research Association for Next generation natural products chemistry
- Development of core technologies for innovative drug development based upon IT(https://www.amed.go.jp/en/program/list/06/01/005.html)

Support by Japan Agency for Medical Research and Development (AMED)

Reference(s)

Article title:

LigandBox : a database for 3D structures of chemical compounds.

Author name(s):

Kawabata,T., Sugihara, Y., Fukunishi, Y., Nakamura, H.

Journal:

BIOPHYSICS,9,113-121.

External Links:

Original website information

Database maintenance site

Technology Research Association for Next generation natural products chemistry

URL of the original website

http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en

Operation start date

Last update date

2018/08/13

URL of the portal site

Whole data download

Referenced database

PDB,KEGG

Entry list

Not available

Query search

Available

Web services

Not available

URL of Web services

Need for user registration

Not available