Novel Memetic Algorithm for Protein Structure Prediction

Authors:
Md. Kamrul Islam;Madhu Chetty
Affiliations:
GSIT, Moansh University, Australia 3842;GSIT, Moansh University, Australia 3842
Venue:
AI '09 Proceedings of the 22nd Australasian Joint Conference on Advances in Artificial Intelligence
Year:
2009

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Abstract

A novel Memetic Algorithm (MA) is proposed for investigating the complex ab initio protein structure prediction problem. The proposed MA has a new fitness function incorporating domain knowledge in the form of two new measures (H-compliance and P-compliance) to indicate hydrophobic and hydrophilic nature of a residue. It also includes two novel techniques for dynamically preserving best fit schema and for providing a guided search. The algorithm performance is investigated with the aid of commonly studied 2D lattice hydrophobic polar (HP) model for the benchmark as well as non-benchmark sequences. Comparative studies with other search algorithms reveal superior performance of the proposed technique.