Protein folding using contact maps.
We discuss the problem of representations of protein structure and give the definition of contact maps. We present a method to obtain a three-dimensional polypeptide conformation from a contact map. We also explain how to deal with the case of nonphysical contact maps. We describe a stochastic method to perform dynamics in contact map space. We explain how the motion is restricted to physical regions of the space. First, we introduce the exact free energy of a contact map and discuss two simple approximations to it. Second, we present a method to derive energy parameters based on perception learning. We prove in an extensive number of situations that the pairwise contact approximation both when alone and when supplemented with a hydrophobic term is unsuitable for stabilizing proteins' native states.
Vendruscolo
M
M
Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel.
Domany
E
E
D007611:Aprotinin / Q000737:chemistry; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D007136:Immunoglobulins / Q000737:chemistry; D008433:Mathematics; D008956:Models, Chemical; D010940:Plant Proteins / Q000737:chemistry; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
D007136:Immunoglobulins; D010940:Plant Proteins; D011506:Proteins; C024934:crambin protein, Crambe abyssinica; D007611:Aprotinin