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A protein-DNA docking benchmark consists of 47 test cases. [17] A protein-RNA docking benchmark was curated as a dataset of 45 non-redundant test cases [18] with complexes solved by X-ray crystallography only as well as an extended dataset of 71 test cases with structures derived from homology modelling as well. [19]
During the course of the docking process, the ligand and the protein adjust their conformation to achieve an overall "best-fit" and this kind of conformational adjustment resulting in the overall binding is referred to as "induced-fit". [5] Molecular docking research focuses on computationally simulating the molecular recognition process.
Signal recognition particle (SRP) receptor, also called the docking protein, is a dimer composed of 2 different subunits that are associated exclusively with the rough ER in mammalian cells. Its main function is to identify the SRP units.
In general, docking protocols are used to predict the interactions between small molecules and proteins. However, docking also can be used to detect associations and binding modes among proteins, peptides, DNA or RNA molecules, carbohydrates, and other macromolecules.
The goal of protein–ligand docking is to predict the position and orientation of a ligand (a small molecule) when it is bound to a protein receptor or enzyme. [1] Pharmaceutical research employs docking techniques for a variety of purposes, most notably in the virtual screening of large databases of available chemicals in order to select ...
In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformational isomerism (conformation) of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion, [1] or protein [2] which binds to the ...
Preparing for molecular docking studies can involve many steps. When docking proteins, proteins are obtained from the Protein Data Bank (PDB), which is an online, open access resources containing the classification, structure/folding, organism, sequence length, mutations, genome, sequence, and other data relating to proteins. [11]
Docking glossary Receptor or host or lock The "receiving" molecule, most commonly a protein or other biopolymer. Ligand or guest or key The complementary partner molecule which binds to the receptor. Ligands are most often small molecules but could also be another biopolymer. Docking Computational simulation of a candidate ligand binding to a ...