In the following, the representation formalism, the fitness function and the genetic operators are described. Then, the results of an ab initio prediction run and of an experiment for side chain placement for the protein Crambin will be discussed. For every application of a genetic algorithm one has to decide on a representation formalism for the genes . This means that the genetic algorithm is configured to operate on numbers, not bit strings as in the original genetic algorithm. A hybrid representation is usually easier to implement and also facilitates the use of domain specific operators.
Binary representations run faster in many applications.
It is not the principal goal of this application to find the single optimal conformation of a protein based on a force field but to generate a small set of native-like conformations . For this task the genetic algorithm is an appropriate tool. For a hybrid representation of proteins one can use Cartesian coordinates, torsion angles, rotamers or a simplified model of residues. For a representation in Cartesian coordinates the 3-dimensional coordinates of all atoms in a protein are recorded. This representation has the advantage of being easily converted to and from the 3-dimensional conformation of a protein.