Simplified models of protein folding exploiting the Lagrange radius of gyration of the hydrophobic component

Abstract

A model is used to emulate a hydrophobic funneling effect in protein folding. Its simple form, introduced as a further interaction term going as the square of the separation distance, is suitable for initial searches of conformational space by parallel computation and special processors which use polynomial presentation of pair-wise interactions. Use of such term implies calculation of the square of the Lagrange radium of gyration, but weighted by hydrophobicity rather than the masses of the constituent particles.