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Comparative Study of Computational Strategies for Protein Structure Prediction

  • Fanny G. Maldonado-NavaEmail author
  • Juan Frausto-Solís
  • Juan Paulo Sánchez-Hernández
  • Juan Javier González Barbosa
  • Ernesto Liñán-García
Chapter
Part of the Studies in Computational Intelligence book series (SCI, volume 749)

Abstract

Protein Folding Problem (PFP) is one of the most challenging problems of combinatorial optimization with applications in bioinformatics and molecular biology. The aim of PFP is to find the three-dimensional structure of a protein, this structure is known as Native Structure (NS), which is characterized by the minimal energy of Gibbs and it is commonly the best functional structure. To find an NS knowing only the amino acids sequence (primary structure) of a protein is known as ab initio problem. A protein can take a huge number of different conformational structures from its primary structure to the NS. For solving PFP, several computational strategies are applied in order to search structures of protein on a huge space of possible solutions. In this work, the most popular methods and strategies are compared, and advantages and disadvantages of them are discussed.

Keywords

Protein folding problem Computational strategies Ab initio Threading Homology 

Notes

Acknowledgements

The authors would like to acknowledge with appreciation and gratitude to CONACYT. Also, acknowledge to Laboratorio Nacional de Tecnologías de la Información (LaNTI) of the Instituto Tecnológico de Ciudad Madero for the access to the cluster. Fanny Gabriela Maldonado-Nava would like to thank CONACYT for the support in the project 429028.

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Copyright information

© Springer International Publishing AG 2018

Authors and Affiliations

  • Fanny G. Maldonado-Nava
    • 1
    Email author
  • Juan Frausto-Solís
    • 1
  • Juan Paulo Sánchez-Hernández
    • 2
  • Juan Javier González Barbosa
    • 1
  • Ernesto Liñán-García
    • 3
  1. 1.TecNM/Instituto Tecnológico de Ciudad MaderoCiudad MaderoMexico
  2. 2.Universidad Politécnica del Estado de MorelosJiutepecMexico
  3. 3.Universidad Autónoma de CoahuilaSaltilloMexico

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