Torsional relaxation for biopolymers

We describe a method for making natural, physical movements in a chained po lymer by sequentially adjusting a few neighboring torsion angles in the pol ymer backbone. In addition to being very fast and easy to implement, the me thod is also very general. It applies equally well to proteins and nucleic acids. This method is then used to design a local refinement procedure. We test the refinement procedure on the minimization of a simple energy functi on for proteins. The energy function has a simplified potential for hydroph obic interaction, a hydrogen-bond term, and a term for van der Waals intera ction. There is considerable current interest in such simple energy functio ns for protein folding, When applied to refine structures found by a global search method, the refinement is able to produce large reduction in the hy drogen-bond term and the van der Waal term of the energy. We conclude that the method is particularly effective in finding good "packing" of residues in an initially compact conformation.