Figure 10. The workflow of the stochastic point cloud method for sampling conformations.

Starting from an initial model comprised of the weighted average coordinates of template structures, its RW energy is calculated as E_old, weighted point clouds are constructed for unfixed residues whose conformations are uncertain. New positions are sampled for unfixed residues from the multivariate normal distribution representing the point clouds, the positions with few or no atom clashes or broken chain are accepted to generate a new model. The new model is accepted based on the difference between its energy E_new and the old energy E_old according to a simulated annealing protocol, and the accepted model is used as the initial model for the next round of modeling, which is repeated until reaching a fixed number of iterations.