TA-PFP: A Transgenetic Algorithm to Solve the Protein Folding Problem

This work reports the application of a transgenetic algorithm to the protein folding problem in the 3D HP model, which is a particular instance of the string folding problem and is known to be NP-hard. The proposed algorithm uses two kinds of plasmids, two kinds of transposons, two information sources, adaptation of parameters and is hybridized with tabu search. The computational experiments consider seven instances of the Tortilla benchmark. The results are favorably comparable with that reported in the literature, attesting the efficiency of the methodology.

[1]  James A. Shapiro,et al.  Transposable elements as the key to a 21st century view of evolution , 2004, Genetica.

[2]  Vincenzo Cutello,et al.  Exploring the Capability of Immune Algorithms: A Characterization of Hypermutation Operators , 2004, ICARIS.

[3]  Frank Thomson Leighton,et al.  Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete , 1998, RECOMB '98.

[4]  L. Margulis.  Symbiosis in cell evolution: Life and its environment on the early earth , 1981 .

[5]  Marco César Goldbarg,et al.  Transgenética computacional: uma aplicação ao problema quadrático de alocação , 2002 .

[6]  K. Dill,et al.  A lattice statistical mechanics model of the conformational and sequence spaces of proteins , 1989 .

[7]  Carlos Cotta,et al.  Protein Structure Prediction Using Evolutionary Algorithms Hybridized with Backtracking , 2009, IWANN.

[8]  B. Bassler,et al.  Quorum sensing: cell-to-cell communication in bacteria. , 2005, Annual review of cell and developmental biology.

[9]  Francisco Dantas,et al.  Piston Pump Mobile Unity Tour Problem: An Evolutionary View , 2002, GECCO Late Breaking Papers.

[10]  Lynn Margulis,et al.  Symbiosis in Cell Evolution: Microbial Communities in the Archean and Proterozoic Eons , 1992 .

[11]  F M Richards,et al.  Areas, volumes, packing and protein structure. , 1977, Annual review of biophysics and bioengineering.

[12]  A. Telser.  Molecular Biology of the Cell, 4th Edition , 2002 .

[13]  J. Skolnick,et al.  Reduced models of proteins and their applications , 2004 .

[14]  J. Davies,et al.  Molecular Biology of the Cell , 1983, Bristol Medico-Chirurgical Journal.

[15]  Vincenzo Cutello,et al.  An Immune Algorithm for Protein Structure Prediction on Lattice Models , 2007, IEEE Transactions on Evolutionary Computation.

[16]  Edmund K. Burke,et al.  Multimeme Algorithms for Protein Structure Prediction , 2002, PPSN.

[17]  P. Grassberger,et al.  Growth algorithms for lattice heteropolymers at low temperatures , 2002, cond-mat/0208042.

[18]  Mihalis Yannakakis,et al.  On the Complexity of Protein Folding , 1998, J. Comput. Biol..

[19]  Jacek Blazewicz,et al.  Application of tabu search strategy for finding low energy structure of protein , 2005, Artif. Intell. Medicine.