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59 relations: Accessible surface area, Agonist, Antagonism (chemistry), Binding site, Bioremediation, Carbohydrate, Comparison of software for molecular mechanics modeling, Conformational isomerism, Decoy, Dihedral angle, Docking@Home, Drug design, Enzyme, Enzyme inhibitor, False positives and false negatives, Feasible region, Flight dynamics, Force field (chemistry), Force field (physics), Genetic algorithm, Gibbs free energy, Granularity, Homology modeling, Ibercivis, IC50, In silico, Katchalski-Katzir algorithm, Lead Finder, Ligand (biochemistry), Lipid, List of molecular graphics systems, List of protein-ligand docking software, Macromolecular docking, Molecular binding, Molecular design software, Molecular dynamics, Molecular mechanics, Molecular modelling, Molecular recognition, Nuclear magnetic resonance spectroscopy of proteins, Nucleic acid, Organic compound, Potency (pharmacology), Protein, Protein Data Bank, Protein design, Protein structure, Receiver operating characteristic, Receptor antagonist, Scoring functions for docking, ..., Search algorithm, Signal transduction, Small molecule, Stochastic, Supramolecular chemistry, Van der Waals surface, Virtual screening, X-ray crystallography, ZINC database. Expand index (9 more) »
Accessible surface area
The accessible surface area (ASA) or solvent-accessible surface area (SASA) is the surface area of a biomolecule that is accessible to a solvent.
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Agonist
An agonist is a chemical that binds to a receptor and activates the receptor to produce a biological response.
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Antagonism (chemistry)
Chemical antagonists impede the normal function of a system.
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Binding site
In biochemistry, a binding site is a region on a protein or piece of DNA or RNA to which ligands (specific molecules and/or ions) may form a chemical bond.
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Bioremediation
Bioremediation is a process used to treat contaminated media, including water, soil and subsurface material, by altering environmental conditions to stimulate growth of microorganisms and degrade the target pollutants.
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Carbohydrate
A carbohydrate is a biomolecule consisting of carbon (C), hydrogen (H) and oxygen (O) atoms, usually with a hydrogen–oxygen atom ratio of 2:1 (as in water); in other words, with the empirical formula (where m may be different from n).
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Comparison of software for molecular mechanics modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
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Conformational isomerism
In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds (refer to figure on single bond rotation).
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Decoy
A decoy is usually a person, device, or event meant as a distraction, to hide what an individual or a group might be looking for.
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Dihedral angle
A dihedral angle is the angle between two intersecting planes.
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Docking@Home
Docking@Home was a distributed computing project hosted by the University of Delaware and running on the Berkeley Open Infrastructure for Network Computing (BOINC) software platform.
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Drug design
Drug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target.
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Enzyme
Enzymes are macromolecular biological catalysts.
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Enzyme inhibitor
4QI9) An enzyme inhibitor is a molecule that binds to an enzyme and decreases its activity.
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False positives and false negatives
In medical testing, and more generally in binary classification, a false positive is an error in data reporting in which a test result improperly indicates presence of a condition, such as a disease (the result is positive), when in reality it is not present, while a false negative is an error in which a test result improperly indicates no presence of a condition (the result is negative), when in reality it is present.
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Feasible region
In mathematical optimization, a feasible region, feasible set, search space, or solution space is the set of all possible points (sets of values of the choice variables) of an optimization problem that satisfy the problem's constraints, potentially including inequalities, equalities, and integer constraints.
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Flight dynamics
Flight dynamics is the study of the performance, stability, and control of vehicles flying through the air or in outer space.
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Force field (chemistry)
In the context of molecular modeling, a force field (a special case of energy functions or interatomic potentials; not to be confused with force field in classical physics) refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics and molecular dynamics simulations.
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Force field (physics)
In physics a force field is a vector field that describes a non-contact force acting on a particle at various positions in space.
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Genetic algorithm
In computer science and operations research, a genetic algorithm (GA) is a metaheuristic inspired by the process of natural selection that belongs to the larger class of evolutionary algorithms (EA).
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Gibbs free energy
In thermodynamics, the Gibbs free energy (IUPAC recommended name: Gibbs energy or Gibbs function; also known as free enthalpy to distinguish it from Helmholtz free energy) is a thermodynamic potential that can be used to calculate the maximum of reversible work that may be performed by a thermodynamic system at a constant temperature and pressure (isothermal, isobaric).
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Granularity
Granularity (also called graininess), the condition of existing in grains or granules, refers to the extent to which a material or system is composed of distinguishable pieces or grains.
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Homology modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template").
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Ibercivis
Ibercivis is a distributed computing platform which allows internet users to participate in scientific research by donating unused computer cycles to run scientific simulations and other tasks.
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IC50
The half maximal inhibitory concentration (IC50) is a measure of the potency of a substance in inhibiting a specific biological or biochemical function.
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In silico
In silico (literally cod Latin for "in silicon", alluding to the mass use of silicon for semiconductor computer chips) is an expression used to mean "performed on computer or via computer simulation." The phrase was coined in 1989 as an allusion to the Latin phrases in vivo, in vitro, and in situ, which are commonly used in biology (see also systems biology) and refer to experiments done in living organisms, outside living organisms, and where they are found in nature, respectively.
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Katchalski-Katzir algorithm
The Katchalski-Katzir algorithm is an algorithm for docking of rigid molecules, developed by Ephraim Katchalski-Katzir, Isaac Shariv and Miriam Eisenstein.
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Lead Finder
Lead Finder software is a computational chemistry application for modeling protein-ligand interactions.
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Ligand (biochemistry)
In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose.
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Lipid
In biology and biochemistry, a lipid is a biomolecule that is soluble in nonpolar solvents.
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List of molecular graphics systems
This is a list of software systems that are used for visualizing macromolecules.
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List of protein-ligand docking software
The number of protein-ligand docking programs currently available is high and has been steadily increasing over the last decades.
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Macromolecular docking
Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules.
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Molecular binding
Molecular binding is an attractive interaction between two molecules that results in a stable association in which the molecules are in close proximity to each other.
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Molecular design software
Molecular design software is software for molecular modeling, that provides special support for developing molecular models de novo.
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Molecular dynamics
Molecular dynamics (MD) is a computer simulation method for studying the physical movements of atoms and molecules.
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Molecular mechanics
Molecular mechanics uses classical mechanics to model molecular systems.
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Molecular modelling
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules.
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Molecular recognition
The term molecular recognition refers to the specific interaction between two or more molecules through noncovalent bonding such as hydrogen bonding, metal coordination, hydrophobic forces, van der Waals forces, π-π interactions, halogen bonding, electrostatic and/or electromagnetic effects.
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Nuclear magnetic resonance spectroscopy of proteins
Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes.
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Nucleic acid
Nucleic acids are biopolymers, or small biomolecules, essential to all known forms of life.
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Organic compound
In chemistry, an organic compound is generally any chemical compound that contains carbon.
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Potency (pharmacology)
In the field of pharmacology, potency is a measure of drug activity expressed in terms of the amount required to produce an effect of given intensity.
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Protein
Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues.
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Protein Data Bank
The Protein Data Bank (PDB) is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids.
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Protein design
Protein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein function.
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Protein structure
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule.
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Receiver operating characteristic
In statistics, a receiver operating characteristic curve, i.e. ROC curve, is a graphical plot that illustrates the diagnostic ability of a binary classifier system as its discrimination threshold is varied.
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Receptor antagonist
A receptor antagonist is a type of receptor ligand or drug that blocks or dampens a biological response by binding to and blocking a receptor rather than activating it like an agonist.
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Scoring functions for docking
In the fields of computational chemistry and molecular modelling, scoring functions are fast approximate mathematical methods used to predict the strength of the non-covalent interaction (also referred to as binding affinity) between two molecules after they have been docked.
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Search algorithm
In computer science, a search algorithm is any algorithm which solves the search problem, namely, to retrieve information stored within some data structure, or calculated in the search space of a problem domain.
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Signal transduction
Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalyzed by protein kinases, which ultimately results in a cellular response.
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Small molecule
Within the fields of molecular biology and pharmacology, a small molecule is a low molecular weight (< 900 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm.
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Stochastic
The word stochastic is an adjective in English that describes something that was randomly determined.
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Supramolecular chemistry
file:Supramolecular Assembly Lehn.jpg |Self-Assembly of a Circular Double Helicate Cucurbituril gyroscope AngewChemIntEd 2002 v41 p275 hires.png|Host-guest complex within another host (cucurbit10uril) Rotaxane Crystal Structure EurJOrgChem page2565 year1998.png| Category:Chemistry.
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Van der Waals surface
The van der Waals surface of a molecule is an abstract representation or model of that molecule, illustrating where, in very rough terms, a surface might reside for the molecule based on the hard cutoffs of van der Waals radii for individual atoms, and it represents a surface through which the molecule might be conceived as interacting with other molecules.
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Virtual screening
Virtual screening (VS) is a computational technique used in drug discovery to search libraries of small molecules in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or enzyme.
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X-ray crystallography
X-ray crystallography is a technique used for determining the atomic and molecular structure of a crystal, in which the crystalline atoms cause a beam of incident X-rays to diffract into many specific directions.
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ZINC database
The ZINC database (recursive acronym: ZINC is not commercial) is a curated collection of commercially available chemical compounds prepared especially for virtual screening.
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Redirects here:
Computational Molecular Docking, Ligand docking, Molecular Docking, Molecular docking, Molecular+Docking.
References
[1] https://en.wikipedia.org/wiki/Docking_(molecular)
