Protein tertiary structure – arrangement of the protein atoms in three-dimensional space.Scoring functions are normally parameterized (or trained) against a data set consisting of experimentally determined binding affinities between molecular species similar to the species that one wishes to predict.įor currently used methods aiming to predict affinities of ligands for proteins the following must first be known or predicted: Lead optimization of screening hits to optimize their affinity and selectivity Ī potentially more reliable but much more computationally demanding alternative to scoring functions are free energy perturbation calculations.De novo design (design "from scratch") of novel small molecules that bind to a protein target.Virtual screening of small molecule databases of candidate ligands to identify novel small molecules that bind to a protein target of interest and therefore are useful starting points for drug discovery.Scoring functions are widely used in drug discovery and other molecular modelling applications. Scoring functions have also been developed to predict the strength of intermolecular interactions between two proteins or between protein and DNA. Most commonly one of the molecules is a small organic compound such as a drug and the second is the drug's biological target such as a protein receptor. In the fields of computational chemistry and molecular modelling, scoring functions are mathematical functions used to approximately predict the binding affinity between two molecules after they have been docked. Docking assessment (DA) Procedure to quantify the predictive capability of a docking protocol. Ranking The process of classifying which ligands are most likely to interact favorably to a particular receptor based on the predicted free-energy of binding. Scoring The process of evaluating a particular pose by counting the number of favorable intermolecular interactions such as hydrogen bonds and hydrophobic contacts. Binding mode The orientation of the ligand relative to the receptor as well as the conformation of the ligand and receptor when bound to each other. Docking Computational simulation of a candidate ligand binding to a receptor. Ligands are most often small molecules but could also be another biopolymer. Ligand or guest or key The complementary partner molecule which binds to the receptor. Receptor or host or lock The "receiving" molecule, most commonly a protein or other biopolymer.
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