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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.
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.
www.schrodinger.com /products /glide Glide is a molecular modeling software for docking of small molecules into proteins and other biopolymers . [ 1 ] [ 2 ] It was developed by Schrödinger, Inc.
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 ...
These partial charges are stationary with respect to the mass of the atom. But molecular dynamics simulations can explicitly model polarizability with the introduction of induced dipoles through different methods, such as Drude particles or fluctuating charges. This allows for a dynamic redistribution of charge between atoms which responds to ...
The quantum-mechanical "Schrödinger's cat" paradox according to the many-worlds interpretation.In this interpretation, every quantum event is a branch point; the cat is both alive and dead, even before the box is opened, but the "alive" and "dead" cats are in different branches of the multiverse, both of which are equally real, but which do not interact with each other.
Thus, after the box is opened and Schroedinger's cat has collapsed to the “alive” state, there still exists a tail of the wavefunction containing “low matter” entity structured like a dead cat. Collapse theorists have offered a range of possible solutions to the structured tails problem, but it remains an open problem. [36]
The successes of kinetic theory gave further credence to the idea that matter is composed of atoms, yet the theory also had shortcomings that would only be resolved by the development of quantum mechanics. [6] The existence of atoms was not universally accepted among physicists or chemists; Ernst Mach, for example, was a staunch anti-atomist. [7]