ChemBioNet recommends ChemAxon tools
For easier cooperation within the ChemBioNet we are going to build an infrastructure based on ChemAxon tools , esp. Instant JChem. Instant JChem is a easy-to-use desktop application for chemists and biologists to work with structures and local or remote chemical databases. It allows sophisticated searches within structures and related tables in a simple and straightforward way and may be easily deployed as data exchange tool between partners of the network. The software is written in Java and runs on all platforms. Instant JChem Personal is free, scientists from academia may apply for a free academic license.
Information on Instant JChem can be found here.
If you have Java Runtime Environment including Webstart installed you may start it following this link. This makes sure that you always use the latest version.
Actual location is: Screening Collections /
ChemBioNet-Collection
This ChemBioNet screening collection is shared with Max-Planck-Institutes (Dresden, Dortmund, Munich) and with Universities and research centers in Germany, Norway and Sweden. This repository will be continuously complemented by compound collections donated by chemists of the network.
The ChemBioNet collection (about 20.000 compounds) has been designed after analysis of the World Drug Index, WDI; for privileged substructures or scaffolds (maximum common substructures) by the drug design and modeling group of the Leibniz-Institut für Molekulare Pharmakologie. The library is placed on 384-well microtiter plates with compounds solubilized at 10 mM concentrations in DMSO (created by ChemDiv). The last two columns of each plate contain only DMSO for set up of controls on the assay plates.
The library contains furthermore about 1200 compounds from the international LOPAC collection of annotated compounds (provided by Sigma Aldrich).
The library is shared with the Leibniz-Institut für Molekulare Pharmakologie (FMP, Berlin), the Helmholtz-Zentrum für Infektionsforschung (former GBF, Braunschweig), the Max-Delbrück-Centrum (MDC, Berlin), the Max-Planck-Institut für Molekulare Physiologie (MPI, Dortmund), several Max-Planck-Institutes from Dresden and Munich, the University of Oslo (Norway) and the Universities of Umea and Göteborg (Sweden). The library has been financed by FMP, GBF and MDC.
Additional libraries of the FMP are:
- NIH sublibraries (about 3.000 compounds)
- Natural Products (HKI, Jena, about 6000 compounds),
- Fragment Library (ChemDiv, 20.000 compounds, all < 310 Dalton).
Structural information for ChemBioNet and LOPAC collections is provided for download as zipped SD-files: ChemBioNet_Web.zip (about 5 Mb)
LOPAC (Library of Pharmacologically Annotated Compounds, Sigma-Aldrich).
Tables are containing compound identifyers (Comp_ID) ordering numbers from providers (ID_Numbers) and location of compounds on plates plus barcodes of ChemBioNet plates (WDI designed, LOPAC and academic partners, about 17.000), the structures and some calculated physico-chemical data.
To search and view the data collection we recommend to use ChemAxon-tools, e.g. Instant JChem .