A new soft-core potential function for molecular dynamics applied to the prediction of protein loop conformations

We have developed a new soft-core potential function for the conformational search of complex systems with molecular dynamics. The potential function was designed to maintain the main equilibrium properties of the original fo rce field, which means that the soft-core potential gives physically realis tic performance also without additional restraints, different from most of the previous soft-core potential functions. The performance of the method w as demonstrated by applying it to the problem of finding native conformatio ns for protein loops. Short loops from neocarzinostatin and parvalbumin wer e used as the first test cases. The use of the new soft-core potential func tion was shown to improve significantly the performance of molecular dynami cs in the search of the native conformation of protein loops. (C) 2000 John Wiley & Sons, Inc.