Torsional angles, molecular

Stein EG, Rice LM, Brunger AT. Torsion-angle molecular dynamics as a new efficient tool for NMR structure calculation. J. Magn. Reson. 1997 124 154-164. 

A set of orientational restraint potentials has been developed for solid-state NMR observables including N chemical shift and N- H dipolar coupling. Torsion angle molecular dynamics (MD) simulations with available experimental N chemical shift and N- H dipolar coupling as target values have been performed to determine orientational information of four membrane proteins and to model the structures of some of these systems in oligomer states. The results suggest that incorporation of the orientational restraint potentials into MD simulations provides an efficient... 

Armen RS, Chen J, Brooks CL III (2009) An evaluation of explicit receptor flexibility in molecular docking using molecular dynamics and torsion angle molecular dynamics. J Chem Theory Comput 5(10) 2909-2923. doi 10.1021/ct900262t... 

X-ray diffraction studies of crystalline samples provide direct information about molecular structure (atoms types and distribution, geometrical parameters, i.e. bond lengths, bond angles and torsion angles, molecular conformation and absolute configuration) and crystal structure (crystal composition, i.e. molecular ratio for complex crystals and/or presence of solvent(s) molecules, intermolecular interactions, especially determination of the networks of hydrogen bmids and short intermolecular contacts). 

Figure 2 Radius of convergence of different refinement methods applied to test refinements with realistic errors added to the initial model. Backbone atom r.m.s. coordinate deviations after refinement are plotted against the starting backbone atom r.m.s. coordinate deviation. The thin dashed line corresponds to refinement by conjugate gradient minimization, the thin solid line corresponds to refinement by slow-cooling simulated annealing using Cartesian molecular dynamics. The thick dot-dashed line corresponds to the average result from ten constant temperature torsion angle molecular dynamics refinements the thick solid line corresponds to the best result from each series of ten refinements...

Figure 5 Average structures from refinements of the DNA dodecamer (CGCGPATTCGCG). (a) Structure produced using Cartesian molecular dynamics simulated annealing, (b) Structure produced using torsion angle molecular dynamics...

You can include geometric restraints—for interatomic distances, bond angles, and torsion angles—in any molecular dynamics calculation or geometry optim i/.ation. Here are some applications of restrain ts ... 

Evalii atm g average distances, angles, and torsion angles, pins their deviations, can facilitate understanding of detailed molecular properties and functional characteristics. 

Example Yon can monitor improper torsion angles to determine wh ich side of a substrate m olecn le faces the active site of a protein. Select three atoms on the substrate molecule and a fourth in the active site. These atom s define an improper torsion angle. Save th is selection as a named selection. Then observe a plot of this improper torsion angle (in the Molecular Dynam ics Results dialog... 

Fig. 7.15 The variation in torsion angles can be effectively represented as a series of dials, where the time corresponds to the distance from the centre of the dial. Data from a molecular dynamics simulation of an intermolecular complex between the enzyme dihydrofolate reductase and a triazine inhibitor [Leach and Klein 1995].

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