Incremental prediction of the side-chain conformation of proteins by a genetic algorithm

The paper reports an approach for predicting the side-chain conformation of a protein using a genetic algorithm: an incremental GA. In the GA, the chromosome consists of an array of side-chain torsion angles(χ), and the fitness is only calculated from overlap among each atom´s van der Waals radius under the assumption of fixed main-chain atoms. The GA was incrementally used in the simulation. No van der Waals contact was observed in the predicted structures. This process automatically conforms most of the large side-chains in the hydrophobic core exactly the same in comparison with physical methods such as X-ray crystallography. This approach shows other solutions than the native tertiary conformation in some small side-chain positions. The observed conformation shows that the incremental GA has abilities in predicting side-chain conformation