Adiabatic map

The reaction modeling techniques described so far (transition structure optimization, adiabatic mapping, and reaction path modeling) rely on the assumption that a single protein structure... 

With the advent of molecular dynamics simulations applied to carbohydrates, one can anticipate the direct computation of more conceptually appealmg surfaces of V in 0s) space from a given U( qint,qext)) in the near future. Monte Carlo integration over (qext) and (b,x, 0h) for fix (0s) provides an alternative procedure, but one which is probably less attractive in terms of efficiency than the molecular dynamics approach. A second alternative, known as adiabatic mapping, provides an approximation to V((0s ), and applications of this method to carbohydrates have recently begun to appear. 12,13 in this approach the conformational... 

Our protocol and the adiabatic mapping procedure described by Ha et al (8) have two features in common. They are both based on molecular mechanics approach, and they both start with several structures scattered at regular intervals over the (( ), j ) space. But the objectives of the approaches are fundamentally different. Whereas the adiabatic mapping procedure is intended to fully characterize the conformational energy surface of disaccharides, our... 

One approach is adiabatic mapping whereby one or two coordinates are identified as dominant within the true reaction coordinate. This might be a single bond that is made or broken in the reaction, or perhaps two such bonds. One then systematically increases or decreases the value of this coordinate(s), while optimizing the energy of the remainder of the system keeping this coordinate frozen. 

A basic means of modelling approximate reaction paths is the adiabatic mapping or coordinate driving approach [123,149]. The energy of the system is calculated by minimizing the energy at a series of fixed (or restrained, e.g. by harmonic forces) values of a reaction coordinate, which may be the distance between two atoms, for example. More extensive and complex combinations of geometrical variables can be chosen. This approach is only valid if one... 

The adiabatic mapping technique used in the lysozyme study has now been... 

Ldemann, S.K., V. Lounnas, and R.C. Wade (2000). How do substrates enter and products exit the buried active site of cytochrome P450cam 2. Steered molecular dynamics and adiabatic mapping of substrate pathways. J. Mol. Biol. 303, 813-830. 

With the QM/MM model of the system constructed, a straightforward means of modeling approximate reaction paths is the adiabatic mapping or coordinate driving approach. The energy of the system is calculated by minimizing the... 

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