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Molecular Simulation Volume 19, 1997 - Issue 4
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Original Articles

Protein Structure Prediction as a Hard Optimization Problem: The Genetic Algorithm Approach

Mehul M. Khimasia Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Madingley Road, Cambridge, CB3 0HE, U.K.
&
Peter V. Coveney Schlumberger Cambridge Research, High Cross, Madingley Road, Cambridge, CB3 0EL, U.K.
Pages 205-226 | Received 01 Feb 1997, Accepted 01 Mar 1997, Published online: 23 Sep 2006

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Marcello Braglia, Davide Castellano & Marco Frosolini. (2016) Joint-replenishment problem under stochastic demands with backorders-lost sales mixtures, controllable lead times, and investment to reduce the major ordering cost. Journal of the Operational Research Society 67:8, pages 1108-1120.
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Barry K. Lavine & Anthony J. Moores. (1999) Genetic Algorithms in Analytical Chemistry. Analytical Letters 32:3, pages 433-445.
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Aimin Yang, Qunwei Zhang, Yikai Liu & Ji Zhao. (2022) The Improvement of DV-Hop Model and Its Application in the Security Performance of Smart Campus. Mathematics 10:15, pages 2663.
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Matti Tedre, Peter Denning & Tapani Toivonen. (2021) CT 2.0. CT 2.0.
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Rumana Nazmul, Madhu Chetty & Ahsan Raja Chowdhury. (2020) Multimodal Memetic Framework for low-resolution protein structure prediction. Swarm and Evolutionary Computation 52, pages 100608.
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Amir Morshedian, Jafar Razmara & Shahriar Lotfi. (2018) A novel approach for protein structure prediction based on an estimation of distribution algorithm. Soft Computing 23:13, pages 4777-4788.
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Sajib Chatterjee, Resheta Ahmed Smrity & Md. Rafiqul Islam. (2016) Protein structure prediction using chemical reaction optimization. Protein structure prediction using chemical reaction optimization.
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Mario Garza-Fabre, Eduardo Rodriguez-Tello & Gregorio Toscano-Pulido. (2015) Constraint-handling through multi-objective optimization: The hydrophobic-polar model for protein structure prediction. Computers & Operations Research 53, pages 128-153.
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Fábio Lima Custódio, Helio J.C. Barbosa & Laurent Emmanuel Dardenne. (2014) A multiple minima genetic algorithm for protein structure prediction. Applied Soft Computing 15, pages 88-99.
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Juan Frausto-Solis, Ernesto Liñan-García, Mishael Sánchez-Pérez & Juan Paulo Sánchez-Hernández. (2014) Chaotic Multiquenching Annealing Applied to the Protein Folding Problem. The Scientific World Journal 2014, pages 1-11.
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Y. Wang, G. D. Guo & L. F. Chen. (2013) Chaotic Artificial Bee Colony algorithm: A new approach to the problem of minimization of energy of the 3D protein structure. Molecular Biology 47:6, pages 894-900.
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Mario Garza-Fabre, Eduardo Rodriguez-Tello & Gregorio Toscano-Pulido. (2013) Comparative Analysis of Different Evaluation Functions for Protein Structure Prediction Under the HP Model. Journal of Computer Science and Technology 28:5, pages 868-889.
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Md. Kamrul Islam & Madhu Chetty. (2013) Clustered Memetic Algorithm With Local Heuristics for Ab Initio Protein Structure Prediction. IEEE Transactions on Evolutionary Computation 17:4, pages 558-576.
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Christiane Regina Soares Brasil, Alexandre Claudio Botazzo Delbem & Fernando Luís Barroso da Silva. (2013) Multiobjective evolutionary algorithm with many tables for purely ab initio protein structure prediction . Journal of Computational Chemistry 34:20, pages 1719-1734.
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Mario Garza-Fabre, Gregorio Toscano-Pulido & Eduardo Rodriguez-Tello. (2013) Handling constraints in the HP model for protein structure prediction by multiobjective optimization. Handling constraints in the HP model for protein structure prediction by multiobjective optimization.
Swakkhar Shatabda, M.A.Hakim Newton, Mahmood A Rashid & Abdul Sattar. (2013) An efficient encoding for simplified protein structure prediction using genetic algorithms. An efficient encoding for simplified protein structure prediction using genetic algorithms.
Camelia Chira & Nima Hatami. 2012. Intelligent Data Engineering and Automated Learning - IDEAL 2012. Intelligent Data Engineering and Automated Learning - IDEAL 2012 184 191 .
Camelia Chira, Dragos Horvath & D Dumitrescu. (2011) Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction. BioData Mining 4:1.
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Camelia Chira. (2011) A hybrid evolutionary approach to protein structure prediction with lattice models. A hybrid evolutionary approach to protein structure prediction with lattice models.
Hesham Awadh A. Bahamish, Rosni Abdullah & Muhannad A. Abu-Hashem. (2010) A modified Marriage in Honey Bee Optimisation (MBO) algorithm for protein structure prediction. A modified Marriage in Honey Bee Optimisation (MBO) algorithm for protein structure prediction.
Hesham Awadh A. Bahamish & Rosni Abdullah. (2010) Prediction of C-peptide structure using artificial bee colony algorithm. Prediction of C-peptide structure using artificial bee colony algorithm.
Camelia Chira, Dragos Horvath & Dumitru Dumitrescu. 2010. Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics. Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics 38 49 .
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R. Santana, P. Larranaga & J.A. Lozano. (2008) Protein Folding in Simplified Models With Estimation of Distribution Algorithms. IEEE Transactions on Evolutionary Computation 12:4, pages 418-438.
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L. Kapsokalivas, X. Gan, A. Albrecht & K. Steinhöfel. 2008. Bioinformatics Research and Development. Bioinformatics Research and Development 167 179 .
Bin Fu & Wei Wang. (2007) Geometric Separators and Their Applications to Protein Folding in the HP-Model. SIAM Journal on Computing 37:4, pages 1014-1029.
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S.K. Pal, S. Bandyopadhyay & S.S. Ray. (2006) Evolutionary computation in bioinformatics: a review. IEEE Transactions on Systems, Man and Cybernetics, Part C (Applications and Reviews) 36:5, pages 601-615.
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Dusan P. Djurdjevic & Mark J. Biggs. (2006) Ab initio protein fold prediction using evolutionary algorithms: Influence of design and control parameters on performance. Journal of Computational Chemistry 27:11, pages 1177-1195.
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David De Sancho, Lidia Prieto, Ana M. Rubio & Antonio Rey. (2005) Evolutionary method for the assembly of rigid protein fragments. Journal of Computational Chemistry 26:2, pages 131-141.
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S. Umezane & S. Fujita. (2005) On Linkage Identification in EC for Solving Combinatorial Optimization Problems. On Linkage Identification in EC for Solving Combinatorial Optimization Problems.
Gabi Escuela, Gabriela Ochoa & Natalio Krasnogor. 2005. Genetic Programming. Genetic Programming 74 84 .
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Harvey J. Greenberg, William E. Hart & Giuseppe Lancia. (2004) Opportunities for Combinatorial Optimization in Computational Biology. INFORMS Journal on Computing 16:3, pages 211-231.
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Roberto Santana, Pedro Larrañaga & José A. Lozano. 2004. Biological and Medical Data Analysis. Biological and Medical Data Analysis 388 398 .
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