DFS-generated pathways in GA crossover for protein structure prediction
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Andrew Lewis | Abdul Sattar | Madhu Chetty | Tamjidul Hoque | Vicky M. Avery | A. Sattar | T. Hoque | V. Avery | A. Lewis | M. Chetty
[1] S. Toma,et al. Contact interactions method: A new algorithm for protein folding simulations , 1996, Protein science : a publication of the Protein Society.
[2] Abdul Sattar,et al. Protein folding prediction in 3D FCC HP lattice model using genetic algorithm , 2007, 2007 IEEE Congress on Evolutionary Computation.
[3] New optimization method for conformational energy calculations on polypeptides: Conformational space annealing , 1997 .
[4] David Corne,et al. Evolutionary Computation In Bioinformatics , 2003 .
[5] H. Scheraga,et al. A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. II. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests. , 1989, Journal of biomolecular structure & dynamics.
[6] Hisao Ishibuchi,et al. Hybrid Evolutionary Algorithms , 2007 .
[7] Konstantinos G. Margaritis,et al. An Experimental Study of Benchmarking Functions for Genetic Algorithms , 2002, Int. J. Comput. Math..
[8] Ron Unger,et al. Genetic Algorithm for 3D Protein Folding Simulations , 1993, ICGA.
[9] Vincenzo Cutello,et al. An Immune Algorithm for Protein Structure Prediction on Lattice Models , 2007, IEEE Transactions on Evolutionary Computation.
[10] Abdul Sattar,et al. Extended HP Model for Protein Structure Prediction , 2009, J. Comput. Biol..
[11] Mihalis Yannakakis,et al. On the complexity of protein folding (abstract) , 1998, RECOMB '98.
[12] Mihalis Yannakakis,et al. On the Complexity of Protein Folding , 1998, J. Comput. Biol..
[13] Shirley Dex,et al. JR 旅客販売総合システム(マルス)における運用及び管理について , 1991 .
[14] Ron Unger,et al. On the applicability of genetic algorithms to protein folding , 1993, [1993] Proceedings of the Twenty-sixth Hawaii International Conference on System Sciences.
[15] Tamjidul Hoque,et al. Fast computation of the fitness function for protein folding prediction in a 2D hydrophilic-hydrophobic model , 2005 .
[16] Mihalis Yannakakis,et al. On the complexity of protein folding (extended abstract) , 1998, STOC '98.
[17] David Baker,et al. Ab initio methods. , 2003, Methods of biochemical analysis.
[18] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197 , 1996 .
[19] L Toma,et al. Folding simulation of protein models on the structure‐based cubo‐octahedral lattice with the Contact Interactions algorithm , 1999, Protein science : a publication of the Protein Society.
[20] Yong Duan,et al. Computational protein folding: From lattice to all-atom , 2001, IBM Syst. J..
[21] Ajay K. Royyuru,et al. Blue Gene: A vision for protein science using a petaflop supercomputer , 2001, IBM Syst. J..
[22] Pedro Larrañaga,et al. Protein Folding in Simplified Models With Estimation of Distribution Algorithms , 2008, IEEE Transactions on Evolutionary Computation.
[23] C. Levinthal. Are there pathways for protein folding , 1968 .
[24] 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.
[25] Ulrich H. E. Hansmann,et al. Protein folding in silico: an overview , 2003, Comput. Sci. Eng..
[26] Bikas K. Chakrabarti,et al. Statistics of linear polymers in disordered media , 2005 .
[27] Jens Meiler,et al. Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation , 2003, Proteins.
[28] R Samudrala,et al. Ab initio construction of protein tertiary structures using a hierarchical approach. , 2000, Journal of molecular biology.
[29] Tom Creighton. Importance of Protein Folding , 2008 .
[30] Richard Bonneau,et al. Ab initio protein structure prediction of CASP III targets using ROSETTA , 1999, Proteins.
[31] D. Baker,et al. Prediction and design of macromolecular structures and interactions , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.
[32] K. Dill,et al. A lattice statistical mechanics model of the conformational and sequence spaces of proteins , 1989 .
[33] D. Baker,et al. A surprising simplicity to protein folding , 2000, Nature.
[34] Andrew Lewis,et al. DFS Based Partial Pathways in GA for Protein Structure Prediction , 2008, PRIB.
[35] V S Pande,et al. Folding pathway of a lattice model for proteins. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[36] Gerard T. Barkema,et al. Exploring high-dimensional energy landscapes , 1999, Comput. Sci. Eng..
[37] R. K. Shyamasundar,et al. Introduction to algorithms , 1996 .
[38] S Banu Ozkan,et al. The protein folding problem: when will it be solved? , 2007, Current opinion in structural biology.
[39] Michael Bachmann,et al. Exact enumeration of three-dimensional lattice proteins , 2005, Comput. Phys. Commun..
[40] K. Lin,et al. Universal amplitude ratios for three-dimensional self-avoiding walks , 2002 .
[41] Julian Lee. Conformational space annealing and a lattice model protein , 2004 .
[42] Madhu Chetty,et al. Generalized Schemata Theorem Incorporating Twin Removal for Protein Structure Prediction , 2007, PRIB.
[43] Holger H. Hoos,et al. An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem , 2005, BMC Bioinformatics.
[44] V. K. Koumousis,et al. A saw-tooth genetic algorithm combining the effects of variable population size and reinitialization to enhance performance , 2006, IEEE Transactions on Evolutionary Computation.
[45] Daniel J. Rigden,et al. From Protein Structure to Function with Bioinformatics , 2009 .
[46] David Corne,et al. An Introduction to Bioinformatics for Computer Scientists , 2003 .
[47] Erich Bornberg-Bauer,et al. Chain growth algorithms for HP-type lattice proteins , 1997, RECOMB '97.
[48] Songde Ma,et al. Protein folding simulations of the hydrophobic–hydrophilic model by combining tabu search with genetic algorithms , 2003 .
[49] Yue,et al. Sequence-structure relationships in proteins and copolymers. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[50] Rolf Backofen,et al. Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets , 1999, Bioinform..
[51] Madhu Chetty,et al. A new guided genetic algorithm for 2D hydrophobic-hydrophilic model to predict protein folding , 2005, 2005 IEEE Congress on Evolutionary Computation.
[52] JEFFREY SKOLNICK. P Computational Studies of Protein Folding B I O E N G I N E E R I N G a N D B I O P H Y S I C S Feasibility of Structural Refinement , 2001 .
[53] Sue Whitesides,et al. A complete and effective move set for simplified protein folding , 2003, RECOMB '03.
[54] K. Dill,et al. The ultimate speed limit to protein folding is conformational searching. , 2007, Journal of the American Chemical Society.
[55] Frank Thomson Leighton,et al. Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete , 1998, RECOMB '98.
[56] Madhu Chetty,et al. A Hybrid Genetic Algorithm for 2D FCC Hydrophobic-Hydrophilic Lattice Model to Predict Protein Folding , 2006, Australian Conference on Artificial Intelligence.
[57] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[58] T. Hales. The Kepler conjecture , 1998, math/9811078.
[59] Keri Schreiner. News: Distributed Projects Tackle Protein Mystery , 2001, IEEE Distributed Syst. Online.
[60] K. Dill. Theory for the folding and stability of globular proteins. , 1985, Biochemistry.
[61] Richard Bonneau,et al. Rosetta in CASP4: Progress in ab initio protein structure prediction , 2001, Proteins.
[62] D. Yee,et al. Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.
[63] T. Head-Gordon,et al. Minimalist models for protein folding and design. , 2003, Current opinion in structural biology.
[64] Erich Bornberg-Bauer,et al. Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[65] Tamjidul Hoque,et al. Significance of Hybrid Evolutionary Computation for Ab Initio Protein Folding Prediction , 2007 .
[66] O. Schueler‐Furman,et al. Progress in Modeling of Protein Structures and Interactions , 2005, Science.
[67] Walter Nadler,et al. Testing a new Monte Carlo algorithm for protein folding , 1998 .
[68] O. Takahashi,et al. Protein Folding by a Hierarchical Genetic Algorithm , 1999 .
[69] Randy L. Haupt,et al. Practical Genetic Algorithms , 1998 .
[70] Sitao Wu,et al. Ab Initio Protein Structure Prediction , 2009 .
[71] Rolf Backofen,et al. Algorithmic approach to quantifying the hydrophobic force contribution in protein folding , 1999, German Conference on Bioinformatics.
[72] Karin M. Verspoor,et al. Protein annotation as term categorization in the gene ontology using word proximity networks , 2005, BMC Bioinformatics.
[73] Jooyoung Lee,et al. New optimization method for conformational energy calculations on polypeptides: Conformational space annealing , 1997, J. Comput. Chem..
[74] Anthony J. Guttmann,et al. Self-avoiding walks in constrained and random geometries: Series studies , 2005 .
[75] Thomas Dandekar,et al. Refined Genetic Algorithm Simulations to Model Proteins , 1999 .
[76] Madhu Chetty,et al. A Guided Genetic Algorithm for Protein Folding Prediction Using 3D Hydrophobic-Hydrophilic Model , 2006, 2006 IEEE International Conference on Evolutionary Computation.
[77] Rolf Backofen,et al. A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models , 2006, Constraints.
[78] W. Wong,et al. Evolutionary Monte Carlo for protein folding simulations , 2001 .
[79] Jim Smith,et al. Study of fitness landscapes for the HP model of protein structure prediction , 2003, The 2003 Congress on Evolutionary Computation, 2003. CEC '03..
[80] Madhu Chetty,et al. Non-Isomorphic Coding in Lattice Model and its Impact for Protein Folding Prediction Using Genetic Algorithm , 2006, 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology.
[81] Ram Samudrala,et al. A Combined Approach for Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence , 1999, Pacific Symposium on Biocomputing.
[82] R Unger,et al. Genetic algorithms for protein folding simulations. , 1992, Journal of molecular biology.
[83] Erich Bornberg-Bauer,et al. Comparing folding codes in simple heteropolymer models of protein evolutionary landscape: robustness of the superfunnel paradigm. , 2005, Biophysical journal.
[84] Kei Yura,et al. [Structural bioinformatics]. , 2009, Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme.