Abstract
This work proposes to optimize Protein Structure Prediction (PSP) using multi-objective ab initio approach. This paper addresses an application of modified NSGA-II (MNSGA-II) by incorporating controlled elitism and Dynamic Crowding Distance (DCD) strategies in NSGA-II for PSP by minimizing free Potential Energy (PE) and minimizing Solvent Accessible Surface area (SAS). In this model, a trigonometric representation is used to compute backbone and side-chain torsion angles of protein atoms. Free energy is calculated using Chemistry at HARvard Macromolecular Mechanics (CHARMm -22). SAS is calculated using dssp program. Both objectives together evaluate the structures of protein conformations. The evolution of protein conformations is directed by optimization of protein energy and surface area contributions using MNSGA-II. To validate the Pareto-front obtained using MNSGA-II, reference Pareto-front is generated using multiple runs of single objective optimization (RGA) with weighted sum of objectives. TOPSIS technique is applied on obtained non-dominated solutions to determine Best Compromise Solution (BCS). Result of MNSGA-II is compared with NSGA-II. The proposed model is validated with Met-enkephalin, a benchmark protein, obtaining very promising results.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
ERCIM News, http://www.ercim.eu/publication/Ercim_News/enw43/bernasconi.html
Cui, Y., Chen, R.S., Hung, W.: Protein folding simulation with genetic algorithm and super secondary structure constraints. Proteins: Structure, Function and Genetics 31, 247–257 (1998)
Unger, R., Moult, J.: Genetic algorithms for protein folding simulations. Biochim. Biophys. 231, 75–81 (1993)
Hoque, T., Chetty, M., Sattar, A.: Extended hp model for protein structure prediction. J. Comput. Biol. 16(1), 85–103 (2009)
Coello, C.A., Van Veldhuizen, D.A., Lamont, G.B.: Evolutionary Algorithms for Solving Multi-Objective Problems. Kluwer Academic Publishers (2002)
Judya, M., Ravichandrana, K., Murugesan, K.: A multi-objective evolutionary algorithm for protein structure prediction with immune operators. Comp. Methods in Biomechanics and Biomedical Engineering 12(4), 407–413 (2009)
Calvo, J.C., Ortega, J.: Parallel protein structure prediction by multiobjective optimization. Parallel, Distributed and Network-based Processing 12(4), 407–413 (2009)
Shi, S.Y.M., Suganthan, N.: Parallel protein structure prediction by multiobjective optimization. KanGAL Report 2004007, 1–7 (2004)
Cutello, V., Narzisi, G., Nicosia, G.: A multi-objective evolutionary approach to the protein structure prediction problem: J. R. Soc. Interface 3, 139–151 (2006)
Chamorro, A.E.M., Divina, F., Aguilar-Ruiz, J.S., Cortés, G.A.: A multi-objective genetic algorithm for the Protein Structure Prediction. In: Intelligent Systems Design and Applications ISDA 2011, pp. 1086–1090 (2011)
NIH Center for Macromolecular Modeling, & Bioinformatics, http://www.ks.uiuc.edu/
Wodak, S.J., Janin, J.: Analytical approximation to the accessible surface area of proteins. Proc. Nati. Acad. Sci. USA 77(4), 1736–1740 (1980)
Centre for Molecular and Biomolecular Informatics, http://swift.cmbi.ru.nl/gv/dssp
Deb, K., Pratap, A., Agarwal, S., Meyarivan, T.: A fast elitist multiobjective genetic algorithm: NSGA-II. IEEE Trans. Evol. Comput. 6(2), 182–197 (2002)
Luo, B., Zheng, J., Xie, J., Wu, J.: Dynamic crowding distance – a new diversity maintenance strategy for MOEAs. In: Proceedings of the IEEE International Conference on Natural Computation, pp. 580–585 (2008)
Jeyadevi, S., Baskar, S., Babulal, C.K., Willjuice Iruthayarajan, M.: Solving multiobjective optimal reactive power dispatch using modified NSGA-II. Int. J of Electrical Power and Energy Systems 33(2), 219–228 (2011)
Kannan, S., Baskar, S., Mccalley, J.D., Murugan, P.: Application of NSGA-II algorithm to generation expansion planning. IEEE Trans. Power System 24(1), 454–461 (2009)
Deb, K., Tewari, R., Dixit, M., Dutta, J.: Finding trade-off solutions close to KKT points using evolutionary multi-objective optimization. IIT Kanpur, KanGAL Report Number 2007006 (2007)
Biological Macromolecular Resource, Protein Data Bank, http://www.pdb.org/
Li, Z., Scheraga, H.A.: Structure and free energy of complex thermodynamic systems. Journal of Molecular Structures 179, 333 (1988)
An open-source molecular visualization system, http://www.pymol.org/
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer International Publishing Switzerland
About this paper
Cite this paper
Sudha, S., Baskar, S., Krishnaswamy, S. (2013). Multi-Objective Approach for Protein Structure Prediction. In: Panigrahi, B.K., Suganthan, P.N., Das, S., Dash, S.S. (eds) Swarm, Evolutionary, and Memetic Computing. SEMCCO 2013. Lecture Notes in Computer Science, vol 8298. Springer, Cham. https://doi.org/10.1007/978-3-319-03756-1_46
Download citation
DOI: https://doi.org/10.1007/978-3-319-03756-1_46
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-03755-4
Online ISBN: 978-3-319-03756-1
eBook Packages: Computer ScienceComputer Science (R0)