Adaptive Simulated Annealing Based Protein Loop Modeling of Neurotoxins

A loop modeling method, adaptive simulated annealing, for ab initio prediction of protein loop structures, as an optimization problem of searching the global minimum of a given energy function, is proposed. An interface-friendly toolbox—LoopModeller in Windows and Linux systems, VC++ and OpenGL environments is developed for analysis and visualization. Simulation results of three short-chain neurotoxins modeled by LoopModeller show that the method proposed is fast and efficient.