CandActBase

This is the base setup of a CandActCFTR-like** Grails server, capable to handle literature and chemical structures.

It contains the necessary grails modules and is set to work directly with an in memory database. You can change this in the settings to use other database systems to store the information of the datasets, e.g. MariaDB.

We use Grails mainly to define the data models to be instantiated within the DB and to create some views to have direct access to overviews without involving external tools. Mayor maintance processing, merging updloading is done with external tools like KNIME using the provided interfaces (either webinterface or direct DB-backend).

CandActCFTR

CandActCFTR is a curated compound database which annotates the chemical structure library with information on where and how in the protein life cycle a compound likely interacts, thus comprising a good starting point for modelling the disease and enhancing ligand based approaches (e.g. via eu-openscreen). In the upcoming extension of CandActCFTR, this ligand-based approach will be complemented by structure-based annotations, including the means to predict the interactions between CandActCFTR substances and CFTR by using existing molecular dynamics trajectories, and by adding more organisation and annotation modules. This approach will help ranking putative therapeutic substances according to their potential to bind CFTR. Moreover, it will be further extended by integrating results from high-throughput screens from collaborators, helping to rank putative therapeutic substances.

Furthermore CandActCFTR will use public gene expression data to assess transcriptome profiles of CandActCFTR substances and compare differentially expressed genes to gene sets with known relevance for CFTR function, helping to rank putative therapeutic substances according to their potential to modify the cellular transcriptome in favor of CFTR function via our Göttingen institutes curated TRANScription FACtor database - TRANSFAC.