To assist structure-based approaches in drug design,
we have processed the PDB to identify binding sites suitable for the docking of a drug-like ligand
and we have so created a database called sc-PDB.
The sc-PDB database provides separated MOL2 files for the ligand, its binding site and the corresponding protein chain(s).
Ions and cofactors at the vicinity of the ligand are included in the protein.
More details about the sc-PDB scope, its content and its evolution during the 2004-2009 period are provided in a pdf document.
Web site specifications :
- PHP/MySQL for database management
- HTML/CSS/AJAX for style and web pages
- VTemplate: A php/HTML template manager
- JQUERY for client-side animation.
- JQUERY-UI for client-side animation.
- chosen plugin (v1.1.0) for form style and multiple selection handling
- Datatable plugin for enhanced results table with the following plugins :
- colvis extension to Dynamically show and hide columns in a table
- TableTools for exports
- PHPExcel to export results table into xlsx file
- Highcharts for interactive charts
- OpenAstexViewer to visualize alignment of proteins in complex with ligands
- ChemAxon Marvin Sketcher and JChem Manager for sketching, storing, and searching molecular structures
