A novel approach has been taken to the problem of protein folding that examines the complete range of accessible folded topologies. The first stage is to generate all possible shapes for a protein of given size and composition. The second procedure is to generate all conformations, with volume exclusion, upon a lattice in a space restricted to the individual compact space. The advantage of this two stage approach is that there is a high efficiency for conformation generation when there are exactly the same number of points as there are residues. The present studies have aimed at a more thorough evaluation of protein folds, with less than atomic detail. The assumption here is that the overall chain tracing is more important than the precise positioning of each atom. Such atomless structures can be evaluated with potential functions that resemble pairwise residue-residue hydrophobicities. These residue-residue potentials are being extended to include repulsive terms appropriate for packing considerations.
NIH ExPorter
NIH ExPorter