Date of Award


Document Type

Campus Access Thesis


Computer Science and Engineering

First Advisor

Jianjun Hu


AutoDock is a widely used automated protein docking program in structure-based drug-design. Different search algorithms, such as Simulated Annealing, traditional Genetic Algorithm and Lamarckian Genetic Algorithm are used in AutoDock. However, the docking performance of these algorithms is still limited by the local optima issue in simulated annealing or the premature convergence issue existing in traditional evolutionary algorithm models. And due to the stochastic nature of the search algorithms, usually users need to do multiple runs to get reasonable docking results, which is time-consuming. We have developed a new docking algorithm AutoDockX by applying a sustainable genetic algorithm named ALPS to the protein docking problem. We tested the docking performances over three different proteins (pr, cox and hsp90) with more than 20 candidate ligands for each protein. Our experiments showed that our sustainable GA based AutodockX gives significantly better docking performance than all the existing search algorithms implemented in the latest version of AutoDock4. Our algorithm also has the benefits of less running time and much higher robustness. Instead of running a genetic algorithm or LGA search many times (e.g. 10), a single run of AutoDockX allows us to get better results. AutodockX thus has unique advantages in large-scale drug-candidate virtual screening in which millions of ligands need to be docked.


© 2009, Emrah Atilgan