Ligand-Protein DataBase: Linking protein-ligand complex structures to binding data

In computational structure-based drug design, the scoring functions are the cornerstones to the success of design/discovery. Many approaches have been explored to improve their reliability and accuracy, leading to three famil ies of scoring functions: force-field-based, knowledge-based, and empirical . The last family is the most widely used in association with docking algor ithms because of its speed, even though such empirical scoring functions pr oduce far too many false positives to be fully reliable. In this work, we d escribe a World Wide Web accessible database that gathers the structural in formation from known complexes of the PDB with experimental binding data. T his database, the Ligand-Protein DataBase (LPDB), is designed to allow the selection of complexes based on various properties of receptors and ligands for the design and parametrization of new scoring functions or to assess a nd improve existing ones. Moreover, for each complex, a continuum of ligand positions ranging from the crystallographic position to points on the surf ace of the protein receptor allows an assessment of the energetic behavior of particular scoring functions.