PROTEIN TERTIARY STRUCTURE PREDICTION BASED ON MAIN CHAIN ANGLE USING A HYBRID BEES COLONY OPTIMIZATION ALGORITHM

作者: ZAKARIA N. MAHMOOD , MASSUDI MAHMUDDIN , MOHAMMED NOORALDEEN MAHMOOD

DOI: 10.1142/S201019451200520X

关键词: Peptide sequenceBiologyA proteinProtein tertiary structureAmino acidImportant researchBioinformaticsHoney BeesProtein structureComputational biologyOptimization algorithm

摘要: Encoding proteins of amino acid sequence to predict classified into their respective families and subfamilies is important research area. However for a given protein, knowing the exact action whether hormonal, enzymatic, transmembranal or nuclear receptors does not depend solely on but way thread folds as well. This study provides prototype system that able protein tertiary structure. Several methods are used develop evaluate produce better accuracy in 3D structure prediction. The Bees Optimization algorithm which inspired from honey bees food foraging method, searching phase. In this study, experiment conducted short have been by previous researches using well-known tools. proposed approach shows promising result.

参考文章(19)
Carl Ivar Branden, John Tooze, Introduction to protein structure ,(1991)
Rolf Backofen, The Protein Structure Prediction Problem: A Constraint Optimization Approach using a New Lower Bound Constraints - An International Journal. ,vol. 6, pp. 223- 255 ,(2001) , 10.1023/A:1011485622743
David S. Goodsell, Arthur J. Olson, Automated docking of substrates to proteins by simulated annealing. Proteins. ,vol. 8, pp. 195- 202 ,(1990) , 10.1002/PROT.340080302
Yan Cui, Run Sheng Chen, Wing Hung Wong, Protein folding simulation with genetic algorithm and supersecondary structure constraints Proteins: Structure, Function, and Genetics. ,vol. 31, pp. 247- 257 ,(1998) , 10.1002/(SICI)1097-0134(19980515)31:3<247::AID-PROT2>3.0.CO;2-G
M. V. Berjanskii, S. Neal, D. S. Wishart, PREDITOR: a web server for predicting protein torsion angle restraints Nucleic Acids Research. ,vol. 34, pp. 63- 69 ,(2006) , 10.1093/NAR/GKL341
Rasmus Fonseca, Martin Paluszewski, Pawel Winter, Protein Structure Prediction Using Bee Colony Optimization Metaheuristic Journal of Mathematical Modelling and Algorithms. ,vol. 9, pp. 181- 194 ,(2010) , 10.1007/S10852-010-9125-1
Stephen Neal, Mark Berjanskii, Haiyan Zhang, David S. Wishart, Accurate prediction of protein torsion angles using chemical shifts and sequence homology. Magnetic Resonance in Chemistry. ,vol. 44, ,(2006) , 10.1002/MRC.1832
Oliviero Carugo, Sándor Pongor, A normalized root-mean-spuare distance for comparing protein three-dimensional structures Protein Science. ,vol. 10, pp. 1470- 1473 ,(2008) , 10.1110/PS.690101
Andrei-José Petrescu, Patrick Calmettes, Dominique Durand, Veronique Receveur, Jeremy C. Smith, Change in backbone torsion angle distribution on protein folding Protein Science. ,vol. 9, pp. 1129- 1136 ,(2000) , 10.1110/PS.9.6.1129
Hesham Awadh A. Bahamish, Rosni Abdullah, Rosalina Abdul Salam, Protein Tertiary Structure Prediction Using Artificial Bee Colony Algorithm asia international conference on modelling and simulation. pp. 258- 263 ,(2009) , 10.1109/AMS.2009.47