Improving Protein Docking Using Efficient Sustainable Evolutionary Algorithm

<p>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.</p>

Name thesis:degree_name

MS

Level thesis:degree_level

Campus Access Thesis

Discipline thesis:degree_discipline

Computer Science and Engineering

Year dc:date.available

2009

Author dc:creator

• Atilgan, Emrah

Contributors dc:contributor

• Jianjun Hu

• Computer Sciences
• Electrical and Computer Engineering
• Engineering
• Physical Sciences and Mathematics
• ALPS
• AutoDock
• drug design
• evolutionary algorithms
• molecular docking
• virtual screening

Statement dc:rights

• © 2009, Emrah Atilgan

Repository record dc:identifier

https://scholarcommons.sc.edu/etd/3

OAI identifier oai:identifier

oai:scholarcommons.sc.edu:etd-1004