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This free-energy map is also known as a potential of mean force (PMF). Free-energy perturbation calculations only converge properly when the difference between the two states is small enough; therefore it is usually necessary to divide a perturbation into a series of smaller "windows", which are computed independently.
The atomic binding energy of the atom is the energy required to disassemble an atom into free electrons and a nucleus. [4] It is the sum of the ionization energies of all the electrons belonging to a specific atom. The atomic binding energy derives from the electromagnetic interaction of the electrons with the nucleus, mediated by photons.
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 binding.
Ligand efficiency is a measurement of the binding energy per atom of a ligand to its binding partner, such as a receptor or enzyme. [1]Ligand efficiency is used in drug discovery research programs to assist in narrowing focus to lead compounds with optimal combinations of physicochemical properties and pharmacological properties.
The atomic binding energy is simply the amount of energy (and mass) released, when a collection of free nucleons are joined to form a nucleus. Nuclear binding energy can be computed from the difference in mass of a nucleus, and the sum of the masses of the number of free neutrons and protons that make up the nucleus.
Calculation of surface energy from first principles (for example, density functional theory) is an alternative approach to measurement. Surface energy is estimated from the following variables: width of the d-band, the number of valence d-electrons, and the coordination number of atoms at the surface and in the bulk of the solid. [5] [page needed]
In thermodynamics, the Gibbs free energy (or Gibbs energy as the recommended name; symbol ) is a thermodynamic potential that can be used to calculate the maximum amount of work, other than pressure–volume work, that may be performed by a thermodynamically closed system at constant temperature and pressure.
The bond dissociation energy (enthalpy) [4] is also referred to as bond disruption energy, bond energy, bond strength, or binding energy (abbreviation: BDE, BE, or D). It is defined as the standard enthalpy change of the following fission: R—X → R + X. The BDE, denoted by Dº(R—X), is usually derived by the thermochemical equation,