LigandBox is a database of 3D compound structures. Compound information is collected from the catalogues of various commercial suppliers, with approved drugs and biochemical compounds taken from KEGG 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. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds.
ligandbox
Local identifiers in LigandBox should match this
regular expression:
^(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$
Compact URIs (CURIEs) constructed from LigandBox should match
this regular expression:
^ligandbox:(HTS|KSH)[0-9]{4}-[0-9]{8}|PDB_[0-9,A-Z]{2,3}|[CD][0-9]{5}$
Mappings from records in Bioregistry to external registries comprises the metaregistry. This resource has 5 mappings to external registries with 2 unique external prefixes.
| Registry Name | Registry Metaprefix | External Prefix | Curate |
|---|---|---|---|
| BioContext | biocontext |
LIGANDBOX
|
|
Integbio
|
integbio |
nbdc00551
|
|
Identifiers.org
|
miriam |
ligandbox
|
|
N2T
|
n2t |
ligandbox
|
|
|
Prefix Commons
|
prefixcommons |
ligandbox
|
A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).
The local unique identifier D00001 is used to demonstrate the providers
available for LigandBox. Some providers may use a different example, which is displayed in the table below.
A guide for curating additional providers can be found
here.
| Provider Name | Provider Code | URI |
|---|---|---|
| LigandBox | ligandbox |
http://www.mypresto5.com/ligandbox/cgi-bin/liginf.cgi?id=D00001 |
| Bioregistry | bioregistry |
https://bioregistry.io/ligandbox:D00001 |
| Identifiers.org | miriam |
https://identifiers.org/ligandbox:D00001 |
| Name-to-Thing | n2t |
https://n2t.net/ligandbox:D00001 |
Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.
| Provider Name | Provider Code | URL |
|---|---|---|
| Bio2RDF | bio2rdf |
http://bio2rdf.org/ligandbox:D00001 |