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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.
Several protein–ligand docking software applications that calculate the site, geometry and energy of small molecules or peptides interacting with proteins are available, such as AutoDock and AutoDock Vina, rDock, FlexAID, Molecular Operating Environment, and Glide. Peptides are a highly flexible type of ligand that has proven to be a ...
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.
The number of notable protein-ligand docking programs currently available is high and has been steadily increasing over the last decades. The following list presents an overview of the most common notable programs, listed alphabetically, with indication of the corresponding year of publication, involved organisation or institution, short description, availability of a webservice and the license.
Molecular docking is extensively used throughout drug discovery for these reasons. [10] Visual representation of molecular docking taking place. A ligand and a receptor or docked in order to determine if the new complex formed is energetically favorable. Preparing for molecular docking studies can involve many steps.
Flexible docking in addition considers all possible conformations of the protein paired with all possible conformations of the ligand. [ 1 ] With present computing resources , it is impossible to exhaustively explore these search spaces; instead, there are many strategies which attempt to sample the search space with optimal efficiency.
Glide is a molecular modeling software for docking of small molecules into proteins and other biopolymers. [1] [2] It was developed by Schrödinger, Inc. References
LeDock is a molecular docking software, designed for protein-ligand interactions, that is compatible with Linux, macOS, and Windows. [ 2 ] [ 3 ] [ 4 ] The software can run as a standalone programme or from Jupyter Notebook . [ 5 ]