@conference{10.1007/978-3-642-29066-4_21b,

title = {A NSGA-II Algorithm for the Residue-Residue Contact Prediction},

author = {A. E. Marquez-Chamorro and F. Divina and J. S. Aguilar-Ruiz and J. Bacardit and G. Asencio-Cortes and C. E. Santiesteban-Toca},

editor = {Giacobini, Mario and Vanneschi, Leonardo and Bush, William S.},

isbn = {978-3-642-29066-4},

year  = {2012},

date = {2012-01-01},

booktitle = {Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics},

pages = {234-244},

publisher = {Springer Berlin Heidelberg},

address = {Berlin, Heidelberg},

abstract = {We present a multi-objective evolutionary approach to predict protein contact maps. The algorithm provides a set of rules, inferring whether there is contact between a pair of residues or not. Such rules are based on a set of specific amino acid properties. These properties determine the particular features of each amino acid represented in the rules. In order to test the validity of our proposal, we have compared results obtained by our method with results obtained by other classification methods. The algorithm shows better accuracy and coverage rates than other contact map predictor algorithms. A statistical analysis of the resulting rules was also performed in order to extract conclusions of the protein folding problem.},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{6121803b,

title = {A multi-objective genetic algorithm for the Protein Structure Prediction},

author = {A. E. Marquez-Chamorro and F. Divina and J. S. Aguilar-Ruiz and G. Asencio-Cortes},

doi = {10.1109/ISDA.2011.6121803},

issn = {2164-7151},

year  = {2011},

date = {2011-11-01},

booktitle = {2011 11th International Conference on Intelligent Systems Design and Applications},

pages = {1086-1090},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{10.1007/978-3-642-19914-1_37b,

title = {Residue-Residue Contact Prediction Based on Evolutionary Computation},

author = {A. E. Marquez-Chamorro and F. Divina and J. S. Aguilar-Ruiz and G. Asencio-Cortes},

editor = {Rocha, Miguel P. and Rodríguez, Juan M. Corchado and Fdez-Riverola, Florentino and Valencia, Alfonso},

isbn = {978-3-642-19914-1},

year  = {2011},

date = {2011-01-01},

booktitle = {5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011)},

pages = {279-283},

publisher = {Springer Berlin Heidelberg},

abstract = {In this study, a novel residue-residue contacts prediction approach based on evolutionary computation is presented. The prediction is based on four amino acids properties. In particular, we consider the hydrophobicity, the polarity, the charge and residues size. The prediction model consists of a set of rules that identifies contacts between amino acids.},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{10.1007/978-3-642-20389-3_10b,

title = {An Evolutionary Approach for Protein Contact Map Prediction},

author = {A. E. Marquez-Chamorro and F. Divina and J. S. Aguilar-Ruiz and G. Asencio-Cortes},

editor = {Pizzuti, Clara and Ritchie, Marylyn D. and Giacobini, Mario},

isbn = {978-3-642-20389-3},

year  = {2011},

date = {2011-01-01},

booktitle = {Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics},

pages = {101-110},

abstract = {In this study, we present a residue-residue contact prediction approach based on evolutionary computation. Some amino acid properties are employed according to their importance in the folding process: hydrophobicity, polarity, charge and residue size. Our evolutionary algorithm provides a set of rules which determine different cases where two amino acids are in contact. A rule represents two windows of three amino acids. Each amino acid is characterized by these four properties. We also include a statistical study for the propensities of contacts between each pair of amino acids, according to their types, hydrophobicity and polarity. Different experiments were also performed to determine the best selection of properties for the structure prediction among the cited properties.},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}

@conference{10.1007/978-3-642-16001-1_31b,

title = {Alpha Helix Prediction Based on Evolutionary Computation},

author = {A. E. Marquez-Chamorro and F. Divina and J. S. Aguilar-Ruiz and G. Asencio-Cortes},

editor = {Dijkstra, Tjeerd M. H. and Tsivtsivadze, Evgeni and Marchiori, Elena and Heskes, Tom},

isbn = {978-3-642-16001-1},

year  = {2010},

date = {2010-01-01},

booktitle = {Pattern Recognition in Bioinformatics},

pages = {358-367},

abstract = {Multiple approaches have been developed in order to predict the protein secondary structure. In this paper, we propose an approach to such a problem based on evolutionary computation. The proposed approach considers various amino acids properties in order to predict the secondary structure of a protein. In particular, we will consider the hydrophobicity, the polarity and the charge of amino acids. In this study, we focus on predicting a particular kind of secondary structure: $alpha$-helices. The results of our proposal will be a set of rules that will identify the beginning or the end of such a structure.},

keywords = {},

pubstate = {published},

tppubtype = {conference}

}