Calculation of protein surface loops using Monte-Carlo simulated annealing simulation

A modified program for protein loop modelling is presented with significant improvements on our previous study (Zhang et al. 1997, Biopolymers, Vol. 41, pp. 61-72), which is capable of sampling the entire conformational space and identifying the low-energy candidates by Monte-Carlo simulated annealing simulation and a cluster analysis method. Twenty flexible surface loops connecting different secondary structures were selected to test the efficiency of this program. The averaged deviations of backbone heavy atoms for four to eight-residue-loops are 0.19, 0.27, 0.46, 0.41 and 0.87 Angstrom respectively. High speed of calculation is achieved with a simplified energy function and a grid-mapping method. As a comparison of single simulation, it takes only four seconds for the simplest four-residue loop and forty-three seconds for the most complex eight-residue loop on a PII-350-Linux platform.