Density functional theoryDensity-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body systems, in particular atoms, molecules, and the condensed phases. Using this theory, the properties of a many-electron system can be determined by using functionals, i.e. functions of another function. In the case of DFT, these are functionals of the spatially dependent electron density.
Docking (molecular)In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction.
Molecular orbital theoryIn chemistry, molecular orbital theory (MO theory or MOT) is a method for describing the electronic structure of molecules using quantum mechanics. It was proposed early in the 20th century. In molecular orbital theory, electrons in a molecule are not assigned to individual chemical bonds between atoms, but are treated as moving under the influence of the atomic nuclei in the whole molecule. Quantum mechanics describes the spatial and energetic properties of electrons as molecular orbitals that surround two or more atoms in a molecule and contain valence electrons between atoms.
Electron densityElectron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial variables and is typically denoted as either or . The density is determined, through definition, by the normalised -electron wavefunction which itself depends upon variables ( spatial and spin coordinates). Conversely, the density determines the wave function modulo up to a phase factor, providing the formal foundation of density functional theory.
Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
Basis set (chemistry)In theoretical and computational chemistry, a basis set is a set of functions (called basis functions) that is used to represent the electronic wave function in the Hartree–Fock method or density-functional theory in order to turn the partial differential equations of the model into algebraic equations suitable for efficient implementation on a computer. The use of basis sets is equivalent to the use of an approximate resolution of the identity: the orbitals are expanded within the basis set as a linear combination of the basis functions , where the expansion coefficients are given by .
Precision and recallIn pattern recognition, information retrieval, object detection and classification (machine learning), precision and recall are performance metrics that apply to data retrieved from a collection, corpus or sample space. Precision (also called positive predictive value) is the fraction of relevant instances among the retrieved instances. Written as a formula:. Recall (also known as sensitivity) is the fraction of relevant instances that were retrieved. Written as a formula: . Both precision and recall are therefore based on relevance.
Accuracy and precisionAccuracy and precision are two measures of observational error. Accuracy is how close a given set of measurements (observations or readings) are to their true value, while precision is how close the measurements are to each other. In other words, precision is a description of random errors, a measure of statistical variability. Accuracy has two definitions: More commonly, it is a description of only systematic errors, a measure of statistical bias of a given measure of central tendency; low accuracy causes a difference between a result and a true value; ISO calls this trueness.
Molecular geometryMolecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determine the position of each atom. Molecular geometry influences several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism and biological activity. The angles between bonds that an atom forms depend only weakly on the rest of molecule, i.
Error correction codeIn computing, telecommunication, information theory, and coding theory, forward error correction (FEC) or channel coding is a technique used for controlling errors in data transmission over unreliable or noisy communication channels. The central idea is that the sender encodes the message in a redundant way, most often by using an error correction code or error correcting code (ECC). The redundancy allows the receiver not only to detect errors that may occur anywhere in the message, but often to correct a limited number of errors.
