Genetic Algorithm inAb Initio Protein Structure Prediction Using Low Resolution Model: A Review
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[1] Ron Unger,et al. Genetic Algorithm for 3D Protein Folding Simulations , 1993, ICGA.
[2] Tamjidul Hoque,et al. Significance of Hybrid Evolutionary Computation for Ab Initio Protein Folding Prediction , 2007 .
[3] Shing-Chung Ngan,et al. PROTINFO: new algorithms for enhanced protein structure predictions , 2005, Nucleic Acids Res..
[4] E. Koonin,et al. A universal trend of amino acid gain and loss in protein evolution , 2005, Nature.
[5] R. Samudrala,et al. De Novo Protein Structure Prediction , 2007 .
[6] David Baker,et al. Ab initio methods. , 2003, Methods of biochemical analysis.
[7] Dieter W. Heermann,et al. Alternative off-lattice model with continuous backbone mass for polymers , 1999 .
[8] O. Schueler‐Furman,et al. Progress in Modeling of Protein Structures and Interactions , 2005, Science.
[9] Lee Aaron Newberg,et al. Exact Calculation of Distributions on Integers, with Application to Sequence Alignment , 2009, J. Comput. Biol..
[10] O. Takahashi,et al. Protein Folding by a Hierarchical Genetic Algorithm , 1999 .
[11] Randy L. Haupt,et al. Practical Genetic Algorithms , 1998 .
[12] Mihalis Yannakakis,et al. On the Complexity of Protein Folding , 1998, J. Comput. Biol..
[13] Yong Duan,et al. Computational protein folding: From lattice to all-atom , 2001, IBM Syst. J..
[14] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[15] Ram Samudrala,et al. PROTINFO: secondary and tertiary protein structure prediction , 2003, Nucleic Acids Res..
[16] Richard Bonneau,et al. Improving the performance of rosetta using multiple sequence alignment information and global measures of hydrophobic core formation , 2001, Proteins.
[17] Erik D. Goodman,et al. A Standard GA Approach to Native Protein Conformation Prediction , 1995 .
[18] T. Schlick. Molecular modeling and simulation , 2002 .
[19] David C. Jones,et al. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. , 1999, Journal of molecular biology.
[20] S. Schulze-Kremer,et al. Genetic algorithms and protein folding. , 2000, Methods in molecular biology.
[21] Ajay K. Royyuru,et al. Blue Gene: A vision for protein science using a petaflop supercomputer , 2001, IBM Syst. J..
[22] M. Vose. The Simple Genetic Algorithm , 1999 .
[23] Xin Yao,et al. Evolutionary computation : theory and applications , 1999 .
[24] Sue Whitesides,et al. A complete and effective move set for simplified protein folding , 2003, RECOMB '03.
[25] 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.
[26] 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.
[27] C. Levinthal. Are there pathways for protein folding , 1968 .
[28] Hisao Ishibuchi,et al. Hybrid Evolutionary Algorithms , 2007 .
[29] Rolf Backofen,et al. Algorithmic approach to quantifying the hydrophobic force contribution in protein folding , 1999, German Conference on Bioinformatics.
[30] Abdul Sattar,et al. AI 2006: Advances in Artificial Intelligence, 19th Australian Joint Conference on Artificial Intelligence, Hobart, Australia, December 4-8, 2006, Proceedings , 2006, Australian Conference on Artificial Intelligence.
[31] P. Grassberger,et al. Testing a new Monte Carlo algorithm for protein folding , 1997, Proteins.
[32] Anthony J. Guttmann,et al. Self-avoiding walks in constrained and random geometries: Series studies , 2005 .
[33] H. Scheraga,et al. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides , 1994 .
[34] Mihalis Yannakakis,et al. On the complexity of protein folding (extended abstract) , 1998, STOC '98.
[35] 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 .
[36] S. Ronald. Duplicate genotypes in a genetic algorithm , 1998, 1998 IEEE International Conference on Evolutionary Computation Proceedings. IEEE World Congress on Computational Intelligence (Cat. No.98TH8360).
[37] D. Baker,et al. Prediction and design of macromolecular structures and interactions , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.
[38] Goldberg,et al. Genetic algorithms , 1993, Robust Control Systems with Genetic Algorithms.
[39] J Skolnick,et al. Predicting leucine zipper structures from sequence. , 1996, Protein engineering.
[40] David E. Goldberg,et al. Genetic Algorithms in Search Optimization and Machine Learning , 1988 .
[41] Erich Bornberg-Bauer,et al. Chain growth algorithms for HP-type lattice proteins , 1997, RECOMB '97.
[42] W. Wong,et al. Evolutionary Monte Carlo for protein folding simulations , 2001 .
[43] William E. Hart,et al. Protein structure prediction with evolutionary algorithms , 1999 .
[44] R Samudrala,et al. Ab initio construction of protein tertiary structures using a hierarchical approach. , 2000, Journal of molecular biology.
[45] Robert G. Reynolds,et al. Evolutionary computation: Towards a new philosophy of machine intelligence , 1997 .
[46] John R. Gunn,et al. Knowledge‐based Prediction of Protein Tertiary Structure , 2002 .
[47] J M Thornton,et al. Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing , 1995, Proteins.
[48] H. L. Tsay,et al. Magnetic field and pressure dependence of T c and T N in TbSr 2 Cu 2.7 Mo 0.3 O 7 − δ , 1999 .
[49] Frank Thomson Leighton,et al. Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete , 1998, RECOMB '98.
[50] Madhu Chetty,et al. Generalized Schemata Theorem Incorporating Twin Removal for Protein Structure Prediction , 2007, PRIB.
[51] Yong Wang,et al. Exploration of two-dimensional hydrophobic-polar lattice model by combining local search with elastic net algorithm. , 2006, The Journal of chemical physics.
[52] Robert S. Germain,et al. Blue matter on blue gene/L: massively parallel computation for biomolecular simulation , 2005, 2005 Third IEEE/ACM/IFIP International Conference on Hardware/Software Codesign and System Synthesis (CODES+ISSS'05).
[53] Holger H. Hoos,et al. An ant colony optimisation algorithm for the 2D and 3D hydrophobic polar protein folding problem , 2005, BMC Bioinformatics.
[54] David Corne,et al. An Introduction to Bioinformatics for Computer Scientists , 2003 .
[55] Richard Bonneau,et al. Ab initio protein structure prediction: progress and prospects. , 2001, Annual review of biophysics and biomolecular structure.
[56] A. Sali,et al. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[57] Chang Wook Ahn,et al. On the practical genetic algorithms , 2005, GECCO '05.
[58] D. Baker,et al. A surprising simplicity to protein folding , 2000, Nature.
[59] Lawrence. Davis,et al. Handbook Of Genetic Algorithms , 1990 .
[60] S. Toma,et al. Contact interactions method: A new algorithm for protein folding simulations , 1996, Protein science : a publication of the Protein Society.
[61] Abdul Sattar,et al. Protein folding prediction in 3D FCC HP lattice model using genetic algorithm , 2007, 2007 IEEE Congress on Evolutionary Computation.
[62] R L Jernigan,et al. Ideal architecture of residue packing and its observation in protein structures , 1997, Protein science : a publication of the Protein Society.
[63] Abdul Sattar,et al. Extended HP Model for Protein Structure Prediction , 2009, J. Comput. Biol..
[64] 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.
[65] Ram Samudrala,et al. A Combined Approach for Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence , 1999, Pacific Symposium on Biocomputing.
[66] L. Darrell Whitley,et al. An overview of evolutionary algorithms: practical issues and common pitfalls , 2001, Inf. Softw. Technol..
[67] R Unger,et al. Genetic algorithms for protein folding simulations. , 1992, Journal of molecular biology.
[68] Lars Malmström,et al. Prediction of CASP6 structures using automated robetta protocols , 2005, Proteins.
[69] Andrzej Kolinski,et al. A unified approach to the prediction of protein structure and function , 2002 .
[70] Thomas Dandekar,et al. Refined Genetic Algorithm Simulations to Model Proteins , 1999 .
[71] 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.
[72] Rolf Backofen,et al. A Constraint-Based Approach to Fast and Exact Structure Prediction in Three-Dimensional Protein Models , 2006, Constraints.
[73] Anthony J. Guttmann,et al. Self-avoiding walks on the simple cubic lattice , 2000 .
[74] Jo Graham,et al. Old and new , 2000 .
[75] G. Crippen. Prediction of protein folding from amino acid sequence over discrete conformation spaces. , 1991, Biochemistry.
[76] David B. Fogel,et al. Evolutionary Computation: Towards a New Philosophy of Machine Intelligence , 1995 .
[77] Gary B. Lamont,et al. Toward Effective Polypeptide Structure Prediction with Parallel Fast Messy Genetic Algorithms , 2003 .
[78] Dominik Gront,et al. Modeling protein structure, dynamics and thermodynamics with reduced representation of conformational space , 2006 .
[79] Mao Chen,et al. Heuristic algorithm for off-lattice protein folding problem , 2006, Journal of Zhejiang University SCIENCE B.
[80] Michael Bachmann,et al. Exact enumeration of three-dimensional lattice proteins , 2005, Comput. Phys. Commun..
[81] K. Lin,et al. Universal amplitude ratios for three-dimensional self-avoiding walks , 2002 .
[82] Songde Ma,et al. Protein folding simulations of the hydrophobic–hydrophilic model by combining tabu search with genetic algorithms , 2003 .
[83] Yue,et al. Sequence-structure relationships in proteins and copolymers. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[84] Rolf Backofen,et al. Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets , 1999, Bioinform..
[85] 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.
[86] 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.
[87] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[88] Yang Zhang,et al. TASSER: An automated method for the prediction of protein tertiary structures in CASP6 , 2005, Proteins.
[89] K. Dill. Theory for the folding and stability of globular proteins. , 1985, Biochemistry.
[90] D. Yee,et al. Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.
[91] John H. Holland,et al. Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence , 1992 .