A Parallel Framework for Multipoint Spiral Search in ab Initio Protein Structure Prediction
暂无分享,去创建一个
[1] Abdul Sattar,et al. Mixed Heuristic Local Search for Protein Structure Prediction , 2013, AAAI.
[2] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[3] María S. Pérez-Hernández,et al. Parallel Stochastic Search for Protein Secondary Structure Prediction , 2003, PPAM.
[4] Abdul Sattar,et al. Memory-based local search for simplified protein structure prediction , 2012, BCB.
[5] 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.
[6] Rabiah Ahmad,et al. Communications in Computer and Information Science , 2010 .
[7] Julio Ortega Lopera,et al. Comparison of parallel multi-objective approaches to protein structure prediction , 2011, The Journal of Supercomputing.
[8] T. Hales. The Kepler conjecture , 1998, math/9811078.
[9] Yang Zhang,et al. The protein structure prediction problem could be solved using the current PDB library. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[10] Z. Luthey-Schulten,et al. Ab initio protein structure prediction. , 2002, Current opinion in structural biology.
[11] El-Ghazali Talbi,et al. A Comparative Study of Parallel Metaheuristics for Protein Structure Prediction on the Computational Grid , 2007, 2007 IEEE International Parallel and Distributed Processing Symposium.
[12] Abdul Sattar,et al. Random-walk: a stagnation recovery technique for simplified protein structure prediction , 2012, BCB '12.
[13] Heitor Silvério Lopes,et al. Parallel Artificial Bee Colony Algorithm Approaches for Protein Structure Prediction Using the 3DHP-SC Model , 2010, IDC.
[14] Abdul Sattar,et al. Protein folding prediction in 3D FCC HP lattice model using genetic algorithm , 2007, 2007 IEEE Congress on Evolutionary Computation.
[15] Andrew Lewis,et al. DFS-generated pathways in GA crossover for protein structure prediction , 2010, Neurocomputing.
[16] Abdul Sattar,et al. Simplified Lattice Models for Protein Structure Prediction: How Good Are They? , 2013, AAAI.
[17] Pascal Van Hentenryck,et al. On Lattice Protein Structure Prediction Revisited , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[18] Abdul Sattar,et al. A New Genetic Algorithm for Simplified Protein Structure Prediction , 2012, Australasian Conference on Artificial Intelligence.
[19] Alessandro Dal Palù,et al. Exploring Protein Fragment Assembly Using CLP , 2011, IJCAI.
[20] 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.
[21] Rolf Backofen,et al. A Constraint-Based Approach to Structure Prediction for Simplified Protein Models That Outperforms Other Existing Methods , 2003, ICLP.
[22] Frank Thomson Leighton,et al. Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete , 1998, RECOMB '98.
[23] Christian Blum,et al. Ant colony optimization: Introduction and recent trends , 2005 .
[24] D. Eisenberg,et al. A method to identify protein sequences that fold into a known three-dimensional structure. , 1991, Science.
[25] Adam Smith. Protein misfolding , 2003, Nature.
[26] S. Colowick,et al. Methods in Enzymology , Vol , 1966 .
[27] Holger H. Hoos,et al. A replica exchange Monte Carlo algorithm for protein folding in the HP model , 2007, BMC Bioinformatics.
[28] Sebastian Will. Constraint-Based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice , 2002, Pacific Symposium on Biocomputing.
[29] Songde Ma,et al. Protein folding simulations of the hydrophobic–hydrophilic model by combining tabu search with genetic algorithms , 2003 .
[30] Yue,et al. Sequence-structure relationships in proteins and copolymers. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[31] Rolf Backofen,et al. CPSP-web-tools: a server for 3D lattice protein studies , 2009, Bioinform..
[32] Abdul Sattar,et al. Spiral search: a hydrophobic-core directed local search for simplified PSP on 3D FCC lattice , 2013, BMC Bioinformatics.
[33] Kathleen Steinhöfel,et al. Protein Folding Simulation by Two-Stage Optimization , 2009 .
[34] Richard Bonneau,et al. Ab initio protein structure prediction of CASP III targets using ROSETTA , 1999, Proteins.
[35] A. Sali,et al. Protein Structure Prediction and Structural Genomics , 2001, Science.
[36] Alessandro Dal Palù,et al. Constraint Logic Programming approach to protein structure prediction , 2004, BMC Bioinformatics.
[37] Ron Unger,et al. Genetic Algorithm for 3D Protein Folding Simulations , 1993, ICGA.
[38] Vincenzo Cutello,et al. An Immune Algorithm for Protein Structure Prediction on Lattice Models , 2007, IEEE Transactions on Evolutionary Computation.
[39] C. Dobson. Protein folding and misfolding , 2003, Nature.
[40] Alessandro Dal Palù,et al. A constraint solver for discrete lattices, its parallelization, and application to protein structure prediction , 2007, Softw. Pract. Exp..
[41] Fred W. Glover,et al. Tabu Search - Part I , 1989, INFORMS J. Comput..
[42] Abdul Sattar,et al. Mixing Energy Models in Genetic Algorithms for On-Lattice Protein Structure Prediction , 2013, BioMed research international.
[43] Abdul Sattar,et al. How Good Are Simplified Models for Protein Structure Prediction? , 2014, Adv. Bioinformatics.
[44] Joe Marks,et al. Human-guided tabu search , 2002, AAAI/IAAI.
[45] Ivan Kondov. Protein structure prediction using distributed parallel particle swarm optimization , 2012, Natural Computing.
[46] El-Ghazali Talbi,et al. A parallel hybrid genetic algorithm for protein structure prediction on the computational grid , 2007, Future Gener. Comput. Syst..
[47] Richard Bonneau,et al. Ab initio protein structure prediction: progress and prospects. , 2001, Annual review of biophysics and biomolecular structure.
[48] R Samudrala,et al. Ab initio construction of protein tertiary structures using a hierarchical approach. , 2000, Journal of molecular biology.
[49] Fred Glover,et al. Tabu Search - Part II , 1989, INFORMS J. Comput..
[50] C. Levinthal. Are there pathways for protein folding , 1968 .
[51] Kathleen Steinhöfel,et al. A hybrid approach to protein folding problem integrating constraint programming with local search , 2010, BMC Bioinformatics.
[52] Alessandro Dal Palù,et al. Heuristics, optimizations, and parallelism for protein structure prediction in CLP(FD) , 2005, PPDP '05.
[53] Charles Seife,et al. What Is the Universe Made Of? , 2005, Science.
[54] Sebastian Will. Exact, constraint-based structure prediction in simple protein models , 2005 .
[55] Julio Ortega Lopera,et al. Parallel Protein Structure Prediction by Multiobjective Optimization , 2009, 2009 17th Euromicro International Conference on Parallel, Distributed and Network-based Processing.
[56] Rolf Backofen,et al. CPSP-tools – Exact and complete algorithms for high-throughput 3D lattice protein studies , 2007, BMC Bioinformatics.
[57] Federico Fogolari,et al. Amino acid empirical contact energy definitions for fold recognition in the space of contact maps , 2003, BMC Bioinformatics.
[58] R. Jernigan,et al. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .
[59] Erik D. Goodman,et al. A Standard GA Approach to Native Protein Conformation Prediction , 1995, ICGA.
[60] Pascal Van Hentenryck,et al. Protein Structure Prediction on the Face Centered Cubic Lattice by Local Search , 2008, AAAI.
[61] Sue Whitesides,et al. A complete and effective move set for simplified protein folding , 2003, RECOMB '03.
[62] Hans-Joachim Böckenhauer,et al. A Local Move Set for Protein Folding in Triangular Lattice Models , 2008, WABI.
[63] El-Ghazali Talbi,et al. A grid-based genetic algorithm combined with an adaptive simulated annealing for protein structure prediction , 2008, Soft Comput..
[64] K. Dill,et al. A lattice statistical mechanics model of the conformational and sequence spaces of proteins , 1989 .
[65] David Baker,et al. Protein Structure Prediction Using Rosetta , 2004, Numerical Computer Methods, Part D.
[66] Fernando Niño,et al. A novel ab-initio genetic-based approach for protein folding prediction , 2007, GECCO '07.
[67] Rolf Backofen,et al. A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models , 2006, Constraints.
[68] So Much More to Know , 2005, Science.
[69] Kathleen Steinhöfel,et al. Population-based local search for protein folding simulation in the MJ energy model and cubic lattices , 2009, Comput. Biol. Chem..