[BioInfo.PL] Ligand.Info: Small-Molecule Meta-Database [Run Ligand.Info]

Ligand.Info is a compilation of various publicly available databases of small molecules such as ChemBank, ChemPDB, KEGG, NCI, AKos GmbH, Asinex Ltd, and TimTec. The total size of the Meta-Database is 1 million entries. The compound records contain calculated three-dimensional coordinates and sometimes information about biological activity. Some molecules have information about FDA drug approving status or about anti-HIV activity. Meta-Database can be downloaded in SDF format and used for virtual high-throughput screening of new potential drugs. The database can also be screened using a Java-based tool.

If you would like to add your compounds to the public Ligand.Info Meta-Database,
please, e-mail: Marcin von Grotthuss ()

Download whole Meta-Database in SDF format

Ligand.Info Meta-Database 1,159,274 entriesgziporzip0.5GB

Download subset of Meta-Database in SDF format

ChemBank subset 2,344 entriesgziporzip 1MB
ChemPDB subset 4,009 entriesgziporzip 1MB
KEGG Ligand subset 10,005 entriesgziporzip 4MB
Anti-HIV NCI subset 42,689 entriesgziporzip 19MB
Drug-likeness NCI subset 192,323 entriesgziporzip 67MB
Not annotated NCI subset 15,237 entriesgziporzip 4MB
AKos GmbH subset 544,391 entriesgziporzip230MB
Asinex Ltd. subset 348,276 entriesgziporzip144MB
TimTec subset 7,500 entriesgziporzip 3MB

Please cite the Meta-Database:
von Grotthuss M, Koczyk G, Pas J, Wyrwicz LS, Rychlewski L
"Ligand.Info Small-Molecule Meta-Database"
Comb Chem High Throughput Screen. 2004 Dec;7(8):757-61. [Library]


Ligand.Info Java-based tool

The Ligand-Info system is based on the assumption that small molecules with similar structure have similar functional (binding) properties. The developed system enables a fast and sensitive structural index based search for similar compounds in large databases. Index profiles, constructed by averaging indexes of related molecules are used to increase the specificity of the search. The utilization of the index profiles helps to focus on frequent, common features of a family of compounds.

The tool can interactively cluster sets of molecules and create index profiles on the user side and automatically download similar molecules from databases. All loaded molecules are automatically displaying using the Marvin viewer. The application requires Netscape 6.0 or IE 5.0 and the Java Runtime Environment 1.3, which can be automatically installed during the first use on MS Windows desktops. Manual installation is required by other systems such as Linux, Solaris, Macintosh, and IRIX.

Please cite the Ligand-Info Applet:
"Ligand-Info, searching for similar small compounds using index profiles."
von Grotthuss M, Pas J, Rychlewski L.
Bioinformatics. 2003 May 22;19(8):1041-2. [Library]

[Run Ligand.Info Now]


Ligand.Info Demo

1. Open file or load demo

2. The first loaded molecule is displaying by the viewer

3. Cluster the whole table using balanced algorithm

4. Choose similarity value for each of the cluster

5. Sort the table in ascending order by Cluster 1 ID

6. Select molecules from Cluster #1

7. Search in Anti-HIV NCI subset of the Meta-Database

8. Download similar molecules to the cluster using profile algorithm

9. Downloaded molecules are selected and sorted by similarity value