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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.
These methods have proven very useful in sampling the vast state-space while maintaining closeness to the actual process involved. Although genetic algorithms are quite successful in sampling the large conformational space, many docking programs require the protein to remain fixed, while allowing only the ligand to flex and adjust to the active ...
Molecular modeling and simulations is a process often used in computational chemistry, but there is wide application for researchers in a variety of fields. This theoretical approach allows scientists to extensively study the properties of molecules, and using the data can provide insight into how these molecules may behave in biological and/or ...
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)
Drug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. [1] The drug is most commonly an organic small molecule that activates or inhibits the function of a biomolecule such as a protein , which in turn results in a ...
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 ...