A NEW-PROTEIN FOLDING RECOGNITION POTENTIAL FUNCTION

On the study of protein inverse folding problem, one goal is to find s imple and efficient potential to evaluate the compatibility between st ructure and a given sequence. We present here a novo empirical mean fo rce potential to address the importance of electrostatic interactions in protein inverse folding study. It is based on protein main chain po lar fraction and constructed in a way similar with Sippl's from a data base of 64 known independent three-dimensional protein structures. Thi s potential was applied to recognize the protein native conformations among a conformation pool. Calculated results show that this potential is powerful in picking out native conformations, in addition it can a lso find structure similarity between proteins with low sequence simil arity. The success of this new potential clearly shows the importance of electrostatic factors in protein inverse folding studies. (C) 1995 Wiley-Liss, Inc.