Protein folding using contact maps and contact vectors

Contact maps and contact vectors are representations of a protein structure particularly suitable for computer simulations of protein folding. We formulate the problem of determining the native state of a protein as one of energy minimization in the space of contact maps or in the space of contact vectors. We first discuss algorithms to explore the portion of contact map and contact vector space that corresponds to the conformational space of a protein. Then we present our results on the feasibility of writing an energy for contact maps and for contact vectors whose ground state corresponds to the native state of a protein. Finally we discuss the possibility of first predicting some of the contacts and then performing a restrained energy minimization in the contact map space or in the contact vector space.