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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.
The Katchalski-Katzir algorithm is an algorithm for docking of rigid molecules, developed by Ephraim Katchalski-Katzir, Isaac Shariv and Miriam Eisenstein. [1] [2]In 1990 Professor Ephraim Katchalski-Katzir, former president of the state of Israel, gathered a group of physicists, chemists and biologists at the Weizmann Institute of Science, to discuss intermolecular recognition.
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.
MacroModel is a computer program for molecular modelling of organic compounds and biopolymers.It features various chemistry force fields, plus energy minimizing algorithms, to predict geometry and relative conformational energies of molecules. [1]
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.
From the equations, the power series must start with at least an order of to satisfy the real part of the equation; for a good classical limit starting with the highest power of the Planck constant possible is preferable, which leads to = = and = = (), with the following constraints on the lowest order terms, () = (()) and () =
Wick rotation connects statistical mechanics to quantum mechanics by replacing inverse temperature with imaginary time, or more precisely replacing 1/k B T with it/ħ, where T is temperature, k B is the Boltzmann constant, t is time, and ħ is the reduced Planck constant.