A Memetic Algorithm for Protein Structure Prediction based on the 2D Triangular Lattice Model

Proteins play fundamental and crucial roles in nearly all biological processes, such as, enzymatic catalysis, signaling transduction, embryonic development, and DNA and RNA synthesis. The main function of the protein is decided by its structure. Therefore, many researchers are interested in the prediction of protein structure. The HP model is one of the commonly used models. But most research on the HP lattice model focuses on how to solve the problem of optimization and ignores the purpose of protein structure prediction, namely the prediction of structure similarity between proteins. The 2D triangular lattice model used in this study can predicate protein structure more closely to its topology compared to the 2D square model commonly used in the past. Besides proposing an effective memetic algorithm (MA), this study also investigated structure similarity of natural proteins.

[1]  Rolf Backofen,et al.  CPSP-web-tools: a server for 3D lattice protein studies , 2009, Bioinform..

[2]  Serafim Batzoglou,et al.  Protein Folding in the Hydrophobic-Polar Model on the 3D Triangular Lattice , 1996 .

[3]  Songde Ma,et al.  Protein folding simulations of the hydrophobic–hydrophilic model by combining tabu search with genetic algorithms , 2003 .

[4]  Pablo Moscato,et al.  On Evolution, Search, Optimization, Genetic Algorithms and Martial Arts : Towards Memetic Algorithms , 1989 .

[5]  Madhu Chetty,et al.  A Hybrid Genetic Algorithm for 2D FCC Hydrophobic-Hydrophilic Lattice Model to Predict Protein Folding , 2006, Australian Conference on Artificial Intelligence.

[6]  Cheng-Jian Lin,et al.  An efficient hybrid of hill-climbing and genetic algorithm for 2D triangular protein structure prediction , 2010, 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW).

[7]  William E. Hart,et al.  Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86% of Optimal , 1997, J. Comput. Biol..

[8]  Edmund K. Burke,et al.  Multimeme Algorithms for Protein Structure Prediction , 2002, PPSN.

[9]  William E. Hart,et al.  Memetic Evolutionary Algorithms , 2005 .

[10]  Holger H. Hoos,et al.  An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem , 2005, BMC Bioinformatics.

[11]  Rolf Backofen,et al.  CPSP-tools – Exact and complete algorithms for high-throughput 3D lattice protein studies , 2008, BMC Bioinformatics.

[12]  Rolf Backofen,et al.  Classifying proteinlike sequences in arbitrary lattice protein models using LatPack , 2008, HFSP journal.

[13]  R Unger,et al.  Genetic algorithms for protein folding simulations. , 1992, Journal of molecular biology.

[14]  Andrew Lewis,et al.  DFS-generated pathways in GA crossover for protein structure prediction , 2010, Neurocomputing.

[15]  Minghui Jiang,et al.  RNA folding on the 3D triangular lattice , 2009, BMC Bioinformatics.

[16]  K. Dill,et al.  A lattice statistical mechanics model of the conformational and sequence spaces of proteins , 1989 .