Abstract
We propose a parallel hybrid genetic algorithm for flexible protein-protein docking in order to improve the conventional “rigid-body” models to manipulate protein-protein interactions. The proposed hybrid algorithm is a combination of an evolutionary algorithm with a simulated annealingo ne, yielding a powerfulp rotein-complexc onformation-searchinegn gine. Parallelization of the procedure makes possible to reach high algorithm performance, in both, execution times and size of treated monomersa nd complexes.K nowledgeo n side chain flexibilityi s extracted by meanso f an exhaustivea nalysiso f crystallographicd ata on proteinsa nd proteinc omplexe.s Results demonstrate the competencyo f the algorithm since comparisono f calculateda nd crystallographic data accounts for a maximumo f 2.5Å in RMS differencei, n cludings ide chain conformation. The system allows routine analysis of this fundamental molecular biology problem important to elucidate bio-macromoleculafru nctioni n biophysicaal nd biochemicaml echanismsi nvolvingm olecular recognitiona nd interaction, y ieldings imultaneouslyc luesf or designingn ew proteins and enzymes directed to different purposes.
