Programa de Pós-graduação em Ciência da Computação
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Navegando Programa de Pós-graduação em Ciência da Computação por Autor "Almeida, Alexandre Barbosa de"
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Item Preditor híbrido de estruturas terciárias de proteínas(Universidade Federal de Goiás, 2023-08-10) Almeida, Alexandre Barbosa de; Soares, Telma Woerle de Lima; http://lattes.cnpq.br/6296363436468330; Soares , Telma Woerle de Lima; Camilo Junior , Celso Gonoalves; Vieira, Flávio Henrique Teles; Delbem, Alexandre Cláudio Botazzo; Faccioli, Rodrigo AntônioProteins are organic molecules composed of chains of amino acids and play a variety of essential biological functions in the body. The native structure of a protein is the result of the folding process of its amino acids, with their spatial orientation primarily determined by two dihedral angles (φ, ψ). This work proposes a new hybrid method for predicting the tertiary structures of proteins called hyPROT, combining techniques of Multi-objective Evolutionary Algorithm optimization (MOEA), Molecular Dynamics, and Recurrent Neural Networks (RNNs). The proposed approach investigates the evolutionary profile of dihedral angles (φ, ψ) obtained by different MOEAs during the minimization process of the objective function by dominance and energy minimization by molecular dynamics. This proposal is unprecedented in the protein prediction literature. The premise under investigation is that the evolutionary profile of dihedrals may be concealing relevant patterns about folding mechanisms. To analyze the evolutionary profile of angles (φ, ψ), RNNs were used to abstract and generalize the specific biases of each MOEA. The selected MOEAs were NSGAII, BRKGA, and GDE3, and the objective function investigated combines the potential energy from non-covalent interactions and the solvation energy. The results obtained show that the hyPROT was able to reduce the RMSD value of the best prediction generated by the MOEAs individually by at least 33%. Predicting new series for dihedral angles allowed for the formation of histograms, indicating the formation of a possible statistical ensemble responsible for the distribution of dihedrals (φ, ψ) during the folding processItem Predição de estrutura terciária de proteínas com técnicas multiobjetivo no algoritmo de monte carlo(Universidade Federal de Goiás, 2016-06-17) Almeida, Alexandre Barbosa de; Faccioli, Rodrigo Antonio; http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4710519J5; Soares, Telma Woerle de Lima; http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4717638T6; Soares, Telma Woerle de Lima; Facciolo, Rodrigo Antonio; Martins, Wellignton Santos; Leão, Salviano de AraújoProteins are vital for the biological functions of all living beings on Earth. However, they only have an active biological function in their native structure, which is a state of minimum energy. Therefore, protein functionality depends almost exclusively on the size and shape of its native conformation. However, less than 1% of all known proteins in the world has its structure solved. In this way, various methods for determining protein structures have been proposed, either in vitro or in silico experiments. This work proposes a new in silico method called Monte Carlo with Dominance, which addresses the problem of protein structure prediction from the point of view of ab initio and multi-objective optimization, considering both protein energetic and structural aspects. The software GROMACS was used for the ab initio treatment to perform Molecular Dynamics simulations, while the framework ProtPred-GROMACS (2PG) was used for the multi-objective optimization problem, employing genetic algorithms techniques as heuristic solutions. Monte Carlo with Dominance, in this sense, is like a variant of the traditional Monte Carlo Metropolis method. The aim is to check if protein tertiary structure prediction is improved when structural aspects are taken into account. The energy criterion of Metropolis and energy and structural criteria of Dominance were compared using RMSD calculation between the predicted and native structures. It was found that Monte Carlo with Dominance obtained better solutions for two of three proteins analyzed, reaching a difference about 53% in relation to the prediction by Metropolis.