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Metadynamics (MTD; also abbreviated as METAD or MetaD) is a computer simulation method in computational physics, chemistry and biology. It is used to estimate the free energy and other state functions of a system , where ergodicity is hindered by the form of the system's energy landscape .
Pose A candidate binding mode. Scoring The process of evaluating a particular pose by counting the number of favorable intermolecular interactions such as hydrogen bonds and hydrophobic contacts. Ranking The process of classifying which ligands are most likely to interact favorably to a particular receptor based on the predicted free-energy of ...
Pose A candidate binding mode. Scoring The process of evaluating a particular pose by counting the number of favorable intermolecular interactions such as hydrogen bonds and hydrophobic contacts. Ranking The process of classifying which ligands are most likely to interact favorably to a particular receptor based on the predicted free-energy of ...
In physics, the Schrödinger picture or Schrödinger representation is a formulation of quantum mechanics in which the state vectors evolve in time, but the operators (observables and others) are mostly constant with respect to time (an exception is the Hamiltonian which may change if the potential changes).
where is position, is the wave function, is a periodic function with the same periodicity as the crystal, the wave vector is the crystal momentum vector, is Euler's number, and is the imaginary unit.
Root Mean Square Deviation is the standard method of evaluating various software performance within the binding mode of the protein-ligand structure. Specifically, it is the root-mean-squared deviation between the software-predicted docking pose of the ligand and the experimental binding mode.
www.deshawresearch.com /resources _desmond.html, schrodinger.com /desmond Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters .
Bust of Schrödinger, in the courtyard arcade of the main building, University of Vienna, Austria Erwin Rudolf Josef Alexander Schrödinger (UK: / ˈ ʃ r ɜː d ɪ ŋ ər, ˈ ʃ r oʊ d ɪ ŋ ər /, US: / ˈ ʃ r oʊ d ɪ ŋ ər /; [3] German: [ˈɛɐ̯vɪn ˈʃʁøːdɪŋɐ]; 12 August 1887 – 4 January 1961), sometimes written as Schroedinger or Schrodinger, was a Nobel Prize–winning ...