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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.
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.
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.
However, the stronger uncertainty relations due to Maccone and Pati provide different uncertainty relations, based on the sum of variances that are guaranteed to be nontrivial whenever the observables are incompatible on the state of the quantum system. [4] (Earlier works on uncertainty relations formulated as the sum of variances include, e.g.,
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]
In quantum mechanics, the Schrödinger equation describes how a system changes with time. It does this by relating changes in the state of the system to the energy in the system (given by an operator called the Hamiltonian). Therefore, once the Hamiltonian is known, the time dynamics are in principle known.
Two of the most used docking programs belong to this class: GOLD [8] and AutoDock. [9] Genetic algorithms allow the exploration of a large conformational space – which is basically spanned by the protein and ligand jointly in this case – by representing each spatial arrangement of the pair as a “gene” with a particular energy.
The following derivation [4] makes use of the Trotter product formula, which states that for self-adjoint operators A and B (satisfying certain technical conditions), we have (+) = (/ /), even if A and B do not commute.