in the prediction of side - chain conformation of protein , conformations are predicted by describing a candidate conformation in the form of an array whose components are the torsion angles of a side chain , subjecting a plurality of solution candidates to evaluation , increasing side chains in a stepwise manner , judging the appropriateness of a solution candidate based upon degree of its van der waals contact , and generating a new solution candidate by changing torsion angle to an arbitrary value or by interchanging the components of the torsion - angle arrays of two solution candidates . further , the foregoing processing is executed with respect to the main - chain conformation whenever a side - chain conformation corresponding to one amino acid residue is constructed , and construction of all side - chain conformations is performed in incremental fashion .