title: NEAT-FLEX: Predicting the conformational flexibility of amino acids using neuroevolution of augmenting topologies.
abstract: The development of computational methods to accurately model three-dimensional protein structures from sequences of amino acid residues is becoming increasingly important to the structural biology field. This paper addresses the challenge of predicting the tertiary structure of a given amino acid sequence, which has been reported to belong to the NP-Complete class of problems. We present a new method, namely NEAT-FLEX, based on NeuroEvolution of Augmenting Topologies (NEAT) to extract structural features from (ABS) proteins that are determined experimentally. The proposed method manipulates structural information from the Protein Data Bank (PDB) and predicts the conformational flexibility (FLEX) of residues of a target amino acid sequence. This information may be used in three-dimensional structure prediction approaches as a way to reduce the conformational search space. The proposed method was tested with 24 different amino acid sequences. Evolving neural networks were compared against a traditional error back-propagation algorithm; results show that the proposed method is a powerful way to extract and represent structural information from protein molecules that are determined experimentally.
authors.affiliation: 1 Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, 91501-970, RS, Brazil.
authors.forename: Bruno
authors.initials: B
authors.lastname: Grisci
authors.affiliation: 1 Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, 91501-970, RS, Brazil.
authors.forename: Márcio
authors.initials: M
authors.lastname: Dorn
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D016571:Neural Networks, Computer; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D011506:Proteins
keywords: Neuroevolution; amino acid flexibility; machine learning in structural bioinformatics; structural bioinformatics; three-dimensional protein structures