Abstract
A protocol using a simulated annealing in four-dimensional space is shown to have excellent sampling properties. In two systems of simulated data, using an unconstrained Ala 30 mer and BPTI, the protocol searches a sufficiently large conformational space and gives complete convergence of the optimization without any trace of initial structure dependence. As a result of an exhaustive sampling, the intrinsic nature of the calculated structures has been revealed. The average of the sampled structures always show a certain pattern of discrepancy from the X-ray structure. This discrepancy is due to the short distance nature of NMR data, and correlates with the characteristic shape of the molecule.
