Abstract: Based on message passing interface (MPI), Autodock code is modified by two parallel methods and applied to dock small molecules XK263 to target HIV-1 protease.The acceleration rate and parallel efficiency are tested with different number of nodes. The improved Autodock codes show a satisfied performance during docking process. Particularly, Scheme Ⅱ has advantages in acceleration rate and parallel efficiency.

Key words: molecular docking, Lamarckian genetic algorithm, message passing interface