docking

http://www.semanticweb.org/ontologies/2010/3/Ontology1271664172453.owl#docking

In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using for example scoring functions. Docking is frequently used to predict the binding orientation of small molecule drug candidates to their protein targets in order to in turn predict the affinity and activity of the small molecule. Hence docking plays an important role in the rational design of drugs. Given the biological and pharmaceutical significance of molecular docking, considerable efforts have been directed towards improving the methods used to predict docking. Predicts the structure of a protein-protein complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions. Exploration of the space of possible protein-ligand geometries. Given: receptor binding pocket and ligand. Task: find correct binding pose. Docking two molecules means constructing the coordinates of the bound state.Bound state is called the complexDocking two molecules means constructing the coordinates of the bound state. Bound state is called the complex.

Ontology1271664172453:docking

docking

Protein-protein interaction http://bioportal.bioontology.org/visualize/39508 Lesk, V., Modeling Protein Complexes. 2006. http://en.wikibooks.org/wiki/Structural_Biochemistry/Molecular_Moldeling/Molecular_Docking

docking dockings molecular docking simulated docking docking simulation docking simulations docking approach docking study docking studies ligand docking protein-ligand docking molecular docking procedure docking procedure

http://www.semanticweb.org/ontologies/2010/3/Ontology1271664172453.owl#structure_based_prediction