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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.
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).
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.
V is the potential energy of the particle (measured relative to any convenient reference level), E is the energy of the particle that is associated with motion in the x-axis (measured relative to V), M(x) is a quantity defined by V(x) − E, which has no accepted name in physics.
where the interaction-picture perturbation Hamiltonian becomes a time-dependent Hamiltonian, unless [H 1,S, H 0,S] = 0. It is possible to obtain the interaction picture for a time-dependent Hamiltonian H 0,S ( t ) as well, but the exponentials need to be replaced by the unitary propagator for the evolution generated by H 0,S ( t ), or more ...
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.
Møller–Plesset perturbation theory (MP) is one of several quantum chemistry post-Hartree–Fock ab initio methods in the field of computational chemistry.It improves on the Hartree–Fock method by adding electron correlation effects by means of Rayleigh–Schrödinger perturbation theory (RS-PT), usually to second (MP2), third (MP3) or fourth (MP4) order.