title: kinDOCK: a tool for comparative docking of protein kinase ligands.
abstract: KinDOCK is a new web server for the analysis of ATP-binding sites of protein kinases. This characterization is based on the docking of ligands already co-crystallized with other protein kinases. A structural library of protein kinase-ligand complexes has been extracted from the Protein Data Bank (PDB). This library can provide both potential ligands and their putative binding orientation for a given protein kinase. After protein-protein structural superposition, the ligands are transferred from the template complexes to the target protein kinase. The resulting complexes are evaluated using the program SCORE to compute a theoretical affinity. They can be dynamically visualized to allow a rapid mapping of important steric clashes and potential substitutions relevant for specificity and affinity. These characteristics allow a quick characterization of protein kinase active sites including conformation changes potentially required to accommodate particular ligands. Additionally, promising pharmacophores can be identified in the focussed library. These features will help to rationalize or optimize virtual screening (VS) on larger chemical compound libraries. The server and its documentation are freely available at http://abcis.cbs.cnrs.fr/kindock/.
authors.affiliation: Atelier de Bio- et Chimie-Informatique Structurale, Centre de Biochimie Structurale, CNRS UMR5048, Montpellier, France.
authors.forename: Laetitia
authors.initials: L
authors.lastname: Martin
authors.forename: Vincent
authors.initials: V
authors.lastname: Catherinot
authors.forename: Gilles
authors.initials: G
authors.lastname: Labesse
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D015195:Drug Design; D020407:Internet; D008024:Ligands; D011487:Protein Conformation; D047428:Protein Kinase Inhibitors / Q000737:chemistry*; D011494:Protein Kinases / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D047428:Protein Kinase Inhibitors; D000255:Adenosine Triphosphate; D011494:Protein Kinases