| simulated annealing, molecular dynamics simulation, torsion angle dynamics, distance and dihedral angle restraints |
The final structure calculations with CYANA were started from 100 conformers with random torsion angle values. Simulated annealing with 10,000 time steps per conformer was done using the DYANA torsion angle dynamics algorithm. Using the FormatConverter, developed as part of the Collaborative Computing Project for the NMR Community (CCPN), the distance and dihedral angle restraints were converted to the X-PLOR restraint format. Subsequently the 100 generated structures were refined using a sh
rt restrained molecular dynamics simulation in explicit solvent in the program XPLOR-NIH. Of these, the 20 lowest energy structures were selected to form the final ensemble. |
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