Spiral search: a hydrophobic-core directed local search for simplified PSP on 3D FCC lattice

BackgroundProtein structure prediction is an important but unsolved problem in biological science. Predicted structures vary much with energy functions and structure-mapping spaces. In our simplified ab initio protein structure prediction methods, we use hydrophobic-polar (HP) energy model for structure evaluation, and 3-dimensional face-centred-cubic lattice for structure mapping. For HP energy model, developing a compact hydrophobic-core (H-core) is essential for the progress of the search. The H-core helps find a stable structure with the lowest possible free energy.ResultsIn order to build H-cores, we present a new Spiral Search algorithm based on tabu-guided local search. Our algorithm uses a novel H-core directed guidance heuristic that squeezes the structure around a dynamic hydrophobic-core centre. We applied random walks to break premature H-cores and thus to avoid early convergence. We also used a novel relay-restart technique to handle stagnation.ConclusionsWe have tested our algorithms on a set of benchmark protein sequences. The experimental results show that our spiral search algorithm outperforms the state-of-the-art local search algorithms for simplified protein structure prediction. We also experimentally show the effectiveness of the relay-restart.

[1]  Fred W. Glover,et al.  Tabu Search - Part I , 1989, INFORMS J. Comput..

[2]  Joe Marks,et al.  Human-guided tabu search , 2002, AAAI/IAAI.

[3]  Ambrish Roy,et al.  Protein Structure Prediction , 2012 .

[4]  Ron Unger,et al.  Genetic Algorithm for 3D Protein Folding Simulations , 1993, ICGA.

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

[6]  Erik D. Goodman,et al.  A Standard GA Approach to Native Protein Conformation Prediction , 1995 .

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

[8]  Charles Seife,et al.  What Is the Universe Made Of? , 2005, Science.

[9]  Sanjay Ranka,et al.  Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine , 2012, BIOINFORMATICS 2012.

[10]  Käthe M. Dahlström.  From protein structure to function with bioinformatics , 2015 .

[11]  Pascal Van Hentenryck,et al.  Protein Structure Prediction on the Face Centered Cubic Lattice by Local Search , 2008, AAAI.

[12]  Sue Whitesides,et al.  A complete and effective move set for simplified protein folding , 2003, RECOMB '03.

[13]  Abdul Sattar,et al.  Protein folding prediction in 3D FCC HP lattice model using genetic algorithm , 2007, 2007 IEEE Congress on Evolutionary Computation.

[14]  Hans-Joachim Böckenhauer,et al.  A Local Move Set for Protein Folding in Triangular Lattice Models , 2008, WABI.

[15]  Pascal Van Hentenryck,et al.  On Lattice Protein Structure Prediction Revisited , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

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

[17]  Yue,et al.  Sequence-structure relationships in proteins and copolymers. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[18]  Richard Bonneau,et al.  Ab initio protein structure prediction: progress and prospects. , 2001, Annual review of biophysics and biomolecular structure.

[19]  R Samudrala,et al.  Ab initio construction of protein tertiary structures using a hierarchical approach. , 2000, Journal of molecular biology.

[20]  Fred Glover,et al.  Tabu Search - Part II , 1989, INFORMS J. Comput..

[21]  C. Dobson.  Protein folding and misfolding , 2003, Nature.

[22]  C. Anfinsen.  Principles that govern the folding of protein chains. , 1973, Science.

[23]  C. Levinthal.  Are there pathways for protein folding , 1968 .

[24]  David Baker,et al.  Protein Structure Prediction Using Rosetta , 2004, Numerical Computer Methods, Part D.

[25]  T. Hales.  The Kepler conjecture , 1998, math/9811078.

[26]  Z. Luthey-Schulten,et al.  Ab initio protein structure prediction. , 2002, Current opinion in structural biology.

[27]  K. Dill.  Theory for the folding and stability of globular proteins. , 1985, Biochemistry.

[28]  Holger H. Hoos,et al.  A replica exchange Monte Carlo algorithm for protein folding in the HP model , 2007, BMC Bioinformatics.

[29]  El-Ghazali Talbi,et al.  A grid-based genetic algorithm combined with an adaptive simulated annealing for protein structure prediction , 2008, Soft Comput..

[30]  Abdul Sattar,et al.  Memory-based local search for simplified protein structure prediction , 2012, BCB.

[31]  E I Shakhnovich,et al.  A test of lattice protein folding algorithms. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Adam Smith.  Protein misfolding , 2003, Nature.

[33]  Andrew Lewis,et al.  Twin Removal in Genetic Algorithms for Protein Structure Prediction Using Low-Resolution Model , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[34]  Christian Blum,et al.  Ant colony optimization: Introduction and recent trends , 2005 .

[35]  Abdul Sattar,et al.  Random-walk: a stagnation recovery technique for simplified protein structure prediction , 2012, BCB '12.

[36]  Andrew Lewis,et al.  DFS-generated pathways in GA crossover for protein structure prediction , 2010, Neurocomputing.