Compact conformations are generated on a lattice by restricting the extent of the chain as it is being generated, in each direction. This procedure enormously reduces the number of conformations, especially when the lattice is densely populated. The intention is to generate most compact conformations and to assess their quality in a general way, based upon what has been observed in globular protein crystal structures. This effectively leads to a """"""""fuzzy"""""""" look at protein conformations, with the major features but not all the details. We will use effective residue- residue interaction energies statistically derived from protein X- ray structures. The way these were obtained was: a lattice-like model is used in which each residue type has a coordination number. If a specific residue has an incompletely filled coordination shell, then it is assumed to be filled with equivalent water molecules. Derived contact energies follow intuition: the most favorably interacting pairs are hydrophobic residues. However, those interactions are quite non-specific. More specificity is observed between polar residues. These energies will be used to assess the qualities of lattice generated conformations. If the procedure yields appropriate conformations, then they can be refined subsequently with energy calculations that include all atoms.
