ABSTRACT
Let us restate the problem in terms of the inputs and expected output of an algorithm that attempts to solve the problem. Since the 3D conformation of the backbone is known, we would have the coordinates of all the alpha carbon atoms, each acting as a point of attachment for a particular side chain. A reasonable approximation is that both the bond lengths and geminal distances within a side chain can be assessed by simply copying these values from side-chain structures previously determined by x-ray analysis. With these assumptions in play, deriving the conformation of a side chain reduces to the determination of the dihedral angles* within the side chain. In summary, the algorithm should determine the settings of the dihedral angles so that the sidechain atoms have 3D positions that will (ideally) yield a global energy minimum.
