3D protein peptide chain search using an improved genetic algorithm

Authors:
Zhenglin Yang;Guirong Liu
Affiliations:
Center for Advanced Computations in Engineering Science, Department of Mechanical Engineering, National University of Singapore, Singapore;Center for Advanced Computations in Engineering Science, Department of Mechanical Engineering, National University of Singapore, Singapore
Venue:
ICCSA'03 Proceedings of the 2003 international conference on Computational science and its applications: PartI
Year:
2003

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Adaptation in natural and artificial systems

Adaptation in natural and artificial systems
A Standard GA Approach to Native Protein Conformation Prediction

Proceedings of the 6th International Conference on Genetic Algorithms

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Abstract

In this paper, an efficient searching algorithm, namely intergeneration projection micro genetic algorithm (IP-µGA) is introduced to search the three dimensional protein conformations. A bond rotation model is developed, in which variables are the dihedral angles along peptide main chain. The root mean square deviation (RMSD) is adopted as the fitness function in the searching process and the template protein structures in protein data bank (PDB) are used for comparison. The results of 3D peptide structures of examples show the effectiveness of present method.