Investigation of the three-dimensional lattice HP protein folding model using a genetic algorithm
AUTOR(ES)
Custódio, Fábio L., Barbosa, Hélio J. C., Dardenne, Laurent E.
FONTE
Genetics and Molecular Biology
DATA DE PUBLICAÇÃO
2004
RESUMO
An approach to the hydrophobic-polar (HP) protein folding model was developed using a genetic algorithm (GA) to find the optimal structures on a 3D cubic lattice. A modification was introduced to the scoring system of the original model to improve the model's capacity to generate more natural-like structures. The modification was based on the assumption that it may be preferable for a hydrophobic monomer to have a polar neighbor than to be in direct contact with the polar solvent. The compactness and the segregation criteria were used to compare structures created by the original HP model and by the modified one. An islands' algorithm, a new selection scheme and multiple-points crossover were used to improve the performance of the algorithm. Ten sequences, seven with length 27 and three with length 64 were analyzed. Our results suggest that the modified model has a greater tendency to form globular structures. This might be preferable, since the original HP model does not take into account the positioning of long polar segments. The algorithm was implemented in the form of a program with a graphical user interface that might have a didactical potential in the study of GA and on the understanding of hydrophobic core formation.
Documentos Relacionados
- Model of protein folding: incorporation of a one-dimensional short-range (Ising) model into a three-dimensional model.
- A simple model for calculating the kinetics of protein folding from three-dimensional structures
- Three-dimensional model of the potyviral genome-linked protein.
- A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
- The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models