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Molecular Simulations
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (a molecular mechanics approach), or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons (a quantum chemistry approach). Molecular mechanics Molecular mechanics is one aspect of molecular modelling, as it involves the use of classic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Internal Coordinates
In chemistry, the Z-matrix is a way to represent a system built of atoms. A Z-matrix is also known as an internal coordinate representation. It provides a description of each atom in a molecule in terms of its atomic number, bond length, bond angle, and dihedral angle, the so-called internal coordinates, although it is not always the case that a Z-matrix will give information regarding bonding since the matrix itself is based on a series of vectors describing atomic orientations in space. However, it is convenient to write a Z-matrix in terms of bond lengths, angles, and dihedrals since this will preserve the actual bonding characteristics. The name arises because the Z-matrix assigns the second atom along the Z axis from the first atom, which is at the origin. Z-matrices can be converted to Cartesian coordinates and back, as the structural information content is identical, the position and orientation in space, however is not meaning the Cartesian coordinates recovered will be ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Comparison Of Software For Molecular Mechanics Modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations. See also *Car–Parrinello molecular dynamics *Comparison of force-field implementations *Comparison of nucleic acid simulation software *List of molecular graphics systems *List of protein structure prediction software *List of quantum chemistry and solid-state physics software * List of software for Monte Carlo molecular modeling * List of software for nanostructures modeling *Molecular design software *Molecular dynamics *Molecular modeling on GPUs *Molecule editor A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, v ... Notes and references External linksSINCRIS [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Comparison Of Nucleic Acid Simulation Software
This is a list of notable computer programs that are used for nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main cl ...s simulations. See also References Computational chemistry software Software comparisons Molecular dynamics software Molecular modelling software {{science-software-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Comparison Of Force Field Implementations
This is a table of notable computer programs implementing molecular mechanics force fields. See also *Force field (chemistry) * List of software for Monte Carlo molecular modeling *Molecular mechanics *Molecular design software *Molecule editor *Comparison of software for molecular mechanics modeling *Molecular modeling on GPU Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations. In 2007, NVIDIA introduced video cards that could be used not only to show graphics but also for scientific calculations. These cards ... References {{Reflist Force fields Molecular modelling Software comparisons ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cheminformatics
Cheminformatics (also known as chemoinformatics) refers to use of physical chemistry theory with computer and information science techniques—so called "''in silico''" techniques—in application to a range of descriptive and prescriptive problems in the field of chemistry, including in its applications to biology and related molecular fields. Such ''in silico'' techniques are used, for example, by pharmaceutical companies and in academic settings to aid and inform the process of drug discovery, for instance in the design of well-defined combinatorial libraries of synthetic compounds, or to assist in structure-based drug design. The methods can also be used in chemical and allied industries, and such fields as environmental science and pharmacology, where chemical processes are involved or studied. History Cheminformatics has been an active field in various guises since the 1970s and earlier, with activity in academic departments and commercial pharmaceutical research and dev ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Catalysis
Catalysis () is the process of increasing the rate of a chemical reaction by adding a substance known as a catalyst (). Catalysts are not consumed in the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recycles quickly, very small amounts of catalyst often suffice; mixing, surface area, and temperature are important factors in reaction rate. Catalysts generally react with one or more reactants to form intermediates that subsequently give the final reaction product, in the process of regenerating the catalyst. Catalysis may be classified as either homogeneous, whose components are dispersed in the same phase (usually gaseous or liquid) as the reactant, or heterogeneous, whose components are not in the same phase. Enzymes and other biocatalysts are often considered as a third category. Catalysis is ubiquitous in chemical industry of all kinds. Estimates are that 90% of all commercially produced chemical products involve catalysts at some s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Enzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called ''enzymology'' and the field of pseudoenzyme analysis recognizes that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts are catalytic RNA molecules, called ribozymes. Enzymes' specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the reaction ra ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Folding
Protein folding is the physical process by which a protein chain is translated to its native three-dimensional structure, typically a "folded" conformation by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA to a linear chain of amino acids. At this stage the polypeptide lacks any stable (long-lasting) three-dimensional structure (the left hand side of the first figure). As the polypeptide chain is being synthesized by a ribosome, the linear chain begins to fold into its three-dimensional structure. Folding of many proteins begins even during translation of the polypeptide chain. Amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein (the right hand side of the figure), ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Z-matrix (chemistry)
In chemistry, the Z-matrix is a way to represent a system built of atoms. A Z-matrix is also known as an internal coordinate representation. It provides a description of each atom in a molecule in terms of its atomic number, bond length, bond angle, and dihedral angle, the so-called internal coordinates, although it is not always the case that a Z-matrix will give information regarding bonding since the matrix itself is based on a series of vectors describing atomic orientations in space. However, it is convenient to write a Z-matrix in terms of bond lengths, angles, and dihedrals since this will preserve the actual bonding characteristics. The name arises because the Z-matrix assigns the second atom along the Z axis from the first atom, which is at the origin. Z-matrices can be converted to Cartesian coordinates and back, as the structural information content is identical, the position and orientation in space, however is not meaning the Cartesian coordinates recovered will be ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Force Field (chemistry)
In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field 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, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both. Force fields are interatomic potentials and utilize the same concept as force fields in classical physics, with the difference that the force field parameters in chemistry describe the energy landscape, from which the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates. ''All-atom'' force fields provide parameters for every type of atom in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular 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. The method is applied mostly in chemical physics, materials science, and biophysics. Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
