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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.
Coarse-grained models are often implemented in the case of protein-peptide docking, as they frequently involve large-scale conformation transitions of the protein receptor. [7] [8] AutoDock is one of the computational tools frequently used to model the interactions between proteins and ligands during the drug discovery process. Although the ...
Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules. Protein–protein complexes are the most commonly attempted targets of such modelling, followed by protein–nucleic acid complexes.
In molecular modelling, docking is a method which predicts the preferred orientation of one molecule to another when bound together in a stable complex. In the case of protein docking , the search space consists of all possible orientations of the protein with respect to the ligand .
Representation of docking a ligand (green) to a protein target (black). Molecular docking (also referred to only as docking) is a method used to predict the orientation coordinates of a molecule when bound to another one (receptor or target). The binding may be mostly through non-covalent interactions while covalently linked binding can also be ...
Some of these techniques include molecular docking, structure-based pharmacophore prediction, and molecular dynamics simulations. [ 17 ] [ 18 ] [ 8 ] Molecular docking is the most used structure-based technique, and it applies a scoring function to estimate the fitness of each ligand against the binding site of the macromolecular receptor ...
The process of evaluating a particular pose by counting the number of favorable intermolecular interactions such as hydrogen bonds and hydrophobic contacts. 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. Docking assessment (DA)
Exocytosis is the process by which a large amount of molecules are released; thus it is a form of bulk transport. Exocytosis occurs via secretory portals at the cell plasma membrane called porosomes. Porosomes are permanent cup-shaped lipoprotein structures at the cell plasma membrane, where secretory vesicles transiently dock and fuse to ...