Protein folding using inter-residue contact

Abstract

Contact maps and contact vectors are representations of a protein structure particularly suitable for computer simulations of protein folding. We first formulate the problem of determining the native state of a protein as one of energy minimization in the space of contact maps or of contact vectors. In order to realize this program we discuss algorithms to explore the portions of contact map space and of contact vector space that correspond to the conformational space of a protein. We then attempt to derive an energy for contact maps or for contact vectors whose ground state corresponds to the native state of a protein and we show that this is an impossible result to achieve. Finally we discuss the possibility of performing protein fold predictions by using database information to predict inter-residue contacts to be used in a restrained energy minimization in the contact map space or in the contact vector space.