The backbone dihedral angles are included in the molecular model of a protein.

Molecular modelling is a collective term that refers to theoretical methods and computational techniques to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying 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 techniques is the atomistic level description of the molecular systems; the lowest level of information is individual atoms (or a small group of atoms). This is in contrast to quantum chemistry (also known as electronic structure calculations) where electrons are considered explicitly. The benefit of molecular modelling is that it reduces the complexity of the system, allowing many more particles (atoms) to be considered during simulations. Image File history File links Size of this preview: 267 × 598 pixel Image in higher resolution (535 × 1198 pixel, file size: 142 KB, MIME type: image/png) I, the creator of this work, hereby release it into the public domain. ... Image File history File links Size of this preview: 267 × 598 pixel Image in higher resolution (535 × 1198 pixel, file size: 142 KB, MIME type: image/png) I, the creator of this work, hereby release it into the public domain. ... In Aerospace engineering, the dihedral is the angle that the two wings make with each other. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... An abstract model (or conceptual model) is a theoretical construct that represents physical, biological or social processes, with a set of variables and a set of logical and quantitative relationships between them. ... In chemistry, a molecule is an aggregate of two or more atoms in a definite arrangement held together by chemical bonds [1] [2] [3] [4] [5]. Chemical substances are not infinitely divisible into smaller fractions of the same substance: a molecule is generally considered the smallest particle of a pure... Computational chemistry is a branch of chemistry that uses the results of theoretical chemistry incorporated into efficient computer programs to calculate the structures and properties of molecules and solids, applying these programs to real chemical problems. ... Computational biology is an interdisciplinary field that applies the techniques of computer science and applied mathematics to problems inspired by biology. ... The Materials Science Tetrahedron, which often also includes Characterization at the center Materials science is an interdisciplinary field involving the properties of matter and its applications to various areas of science and engineering. ... Quantum chemistry is a branch of theoretical chemistry, which applies quantum mechanics and quantum field theory to address issues and problems in chemistry. ...

Molecular mechanics is one aspect of molecular modelling, as it is refers to the use of classical mechanics/Newtonian mechanics to describe the physical basis behind the models. Molecular models typically describe atoms (nucleus and electrons collectively) as point charges with an associated mass. The interactions between neighbouring atoms are described by spring-like interactions (representing chemical bonds) and van der Waals forces. The Lennard-Jones potential is commonly used to describe van der Waals forces. The electostatic interactions are computed based on Coulomb's law. Atoms are assigned coordinates in Cartesian space or in internal coordinates, and can also be assigned velocities in dynamical simulations. The atomic velocities are related to the temperature of the system, a macroscopic quantity. The collective mathematical expression is known as a potential function and is related to the system internal energy (U), a thermodynamic quantity equal to the sum of potential and kinetic energies. Methods which minimize the potential energy are known as energy minimization techniques (e.g., steepest descent and conjugate gradient), while methods that model the behaviour of the system with propagation of time are known as molecular dynamics. The term molecular mechanics refers to the use of Newtonian mechanics to model molecular systems. ... Classical mechanics is a branch of physics which studies the deterministic motion of objects. ... It has been suggested that this article or section be merged with Classical mechanics. ... In chemistry, a chemical bond is the force which holds together atoms in molecules or crystals. ... The title given to this article is incorrect due to technical limitations. ... Neutral atoms and molecules are subject to two distinct forces in the limit of large distance, and short distance: an attractive van der Waals force, or dispersion force, at long ranges, and a repulsion force, the result of overlapping electron orbitals, referred to as Pauli repulsion (from Pauli exclusion principle). ... The title given to this article is incorrect due to technical limitations. ... Coulombs torsion balance In physics, Coulombs law is an inverse-square law indicating the magnitude and direction of electrostatic force that one stationary, electrically charged object of small dimensions (ideally, a point source) exerts on another. ... There are apparentlly two uses for the term Z-matrix. ... The term potential function can mean more than one thing. ... Gradient descent is an optimization algorithm that approaches a local maximum of a function by taking steps proportional to the gradient (or the approximate gradient) of the function at the current point. ... In mathematics, the conjugate gradient method is an algorithm for the numerical solution of particular systems of linear equations, namely those whose matrix is symmetric and positive definite. ... Molecular dynamics (MD) is a form of computer simulation where atoms and molecules are allowed to interact for a period of time under known laws of physics. ...

E = E_bonds + E_angle + E_dihedral + E_{non − bonded}

E_{non − bonded} = E_{electrostatic} + E_vanderWaals

This function, referred to as a potential function, computes the molecular potential energy as a sum of energy terms that describe the deviation of bond lengths, bond angles and torsion angles away from equilibrium values, plus terms for non-bonded pairs of atoms describing van der Waals and electrostatic interactions. The set of parameters consisting of equilibrium bond lengths, bond angles, partial charge values, force constants and van der Waals parameters are collectively known as a force field. Different implementations of molecular mechanics use slightly different mathematical expressions, and therefore, different constants for the potential function. The common force fields in use today have been developed by using high level quantum calculations and/or fitting to experimental data. The technique known as energy minimization is used to find positions of zero gradient for all atoms, in other words, a local energy minimum. Lower energy states are more stable and are commonly investigated because of their role in chemical and biological processes. A molecular dynamics simulation, on the other hand, computes the behaviour of a system as a function of time. It involves solving Newton's laws of motion, principally the second law, F = ma. Integration of Newton's laws of motion, using different integration algorithms, leads to atomic trajectories in space and time. The force on an atom is defined as the negative gradient of the potential energy function. The energy minimization technique is useful for obtaining a static picture for comparing between states of similar systems, while molecular dynamics provides information about the dynamic processes with the intrinsic inclusion of temperature effects. The term potential function can mean more than one thing. ... It has been suggested that this article or section be merged with force field (physics). ... The term potential function can mean more than one thing. ... Molecular dynamics (MD) is a form of computer simulation where atoms and molecules are allowed to interact for a period of time under known laws of physics. ...

Molecules can be modelled either in vacuum or in the presence of a solvent such as water. Simulations of systems in vacuum are referred to as gas-phase simulations, while those that include the presence of solvent molecules are referred to as explicit solvent simulations. In another type of simulation, the effect of solvent is estimated using an empirical mathematical expression; these are known as implicit solvation simulations.

Molecular modelling methods are now routinely used to investigate the structure, dynamics and thermodynamics of inorganic, biological, and polymeric systems. The types of biological activity that have been investigated using molecular modelling include protein folding, enzyme catalysis, protein stability, conformational changes associated with biomolecular function, and molecular recognition of proteins, DNA, and membrane complexes. Protein folding is the process by which a protein assumes its characteristic functional shape or tertiary structure, also known as the native state. ... Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... In chemistry and biology, catalysis is the acceleration (increase in rate) or slowing down of a chemical reaction by means of a substance, called a catalyst, that is itself not consumed by the overall reaction. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ...

Popular software for molecular modelling

• Millsian
• BALLView
• Cerius2
• InsightII
• Sybyl
• MOE
• Ghemical
• MMTK
• Molsoft ICM
• PyMOL
• VMD
• SPARTAN
• GROMOS
• GAUSSIAN

BALLView is an application written in Python for molecular modeling and visualizing molecular models. ... Ghemical is a computational chemistry software package written in C++ and released under the GNU GPL. The program has GUI based on GTK+2 and supports quantum mechanical and molecular mechanic models, with geometry optimization, molecular dynamics, and a large set of visualization tools. ... The Molecular Modelling Toolkit (MMTK) is an open source software package written in Python, which performs common tasks in molecular modelling. ... PyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. ... Screenshot of VMD 1. ... GROMOS is a force field for molecular dynamics developed at the University of Groningen and the ETH Zurich. ... Generally, the word gaussian pertains to Carl Friedrich Gauss and his ideas. ...

See also

• Cheminformatics
• Computational chemistry
• Molecular dynamics
• Molecular graphics
• Molecular mechanics
• Molecular model
• Monte Carlo method
• Force field

Cheminformatics (also known as chemoinformatics and chemical informatics) is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. ... Computational chemistry is a branch of chemistry that uses the results of theoretical chemistry incorporated into efficient computer programs to calculate the structures and properties of molecules and solids, applying these programs to real chemical problems. ... Molecular dynamics (MD) is a form of computer simulation where atoms and molecules are allowed to interact for a period of time under known laws of physics. ... Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. ... The term molecular mechanics refers to the use of Newtonian mechanics to model molecular systems. ... This page meets Wikipedias criteria for speedy deletion. ... Monte Carlo methods are a widely used class of computational algorithms for simulating the behavior of various physical and mathematical systems, and for other computations. ... It has been suggested that this article or section be merged with force field (physics). ...

External links

• Center for Molecular Modeling at NIH
• Molecular Simulation

References

• A.R. Leach, Molecular Modelling: Principles and Applications, 2001, ISBN 0-582-38210-6
• Daan Frenkel, Berend Smit Understanding Molecular Simulation: From Algorithms to Applications, 1996, ISBN 0-12-267370-0