GEM: A Gaussian evolutionary method for predicting protein side‐chain conformations
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Cheng-Yan Kao | Ming-Jing Hwang | Chi-Hung Tsai | Jenn-Kang Hwang | Huai-Kuang Tsai | Jinn-Moon Yang | Jenn-Kang Hwang | Cheng-Yan Kao | Jinn-Moon Yang | M. Hwang | Huai-Kuang Tsai | Chi-Hung Tsai
[1] S. Subbiah,et al. Prediction of protein side-chain conformation by packing optimization. , 1991, Journal of molecular biology.
[2] Jinn-Moon Yang,et al. Integrating adaptive mutations and family competition into genetic algorithms as function optimizer , 2000, Soft Comput..
[3] R. Samudrala,et al. Determinants of side chain conformational preferences in protein structures. , 1998, Protein engineering.
[4] David E. Goldberg,et al. Genetic Algorithms in Search Optimization and Machine Learning , 1988 .
[5] P. Koehl,et al. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. , 1994, Journal of molecular biology.
[6] Cheng-Yan Kao,et al. A Genetic Algorithm with Adaptive Mutations and Family Competition for Training Neural Networks , 2000, Int. J. Neural Syst..
[7] Cheng-Yan Kao,et al. An evolutionary algorithm for the synthesis of multilayer coatings at oblique light incidence , 2001 .
[8] Johan Desmet,et al. The dead-end elimination theorem and its use in protein side-chain positioning , 1992, Nature.
[9] N. Grishin,et al. Side‐chain modeling with an optimized scoring function , 2002, Protein science : a publication of the Protein Society.
[10] R. Lavery,et al. A new approach to the rapid determination of protein side chain conformations. , 1991, Journal of biomolecular structure & dynamics.
[11] J. K. Hwang,et al. Side-chain prediction by neural networks and simulated annealing optimization. , 1995, Protein engineering.
[12] P. Argos,et al. Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins. , 1993, Journal of molecular biology.
[13] M. Levitt. Protein folding by restrained energy minimization and molecular dynamics. , 1983, Journal of molecular biology.
[14] C. Laughton,et al. Prediction of protein side-chain conformations from local three-dimensional homology relationships. , 1994, Journal of molecular biology.
[15] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .
[16] J. Mendes,et al. Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction. , 1999, Biopolymers.
[17] A. Leach,et al. Ligand docking to proteins with discrete side-chain flexibility. , 1994, Journal of molecular biology.
[18] Z. Xiang,et al. Extending the accuracy limits of prediction for side-chain conformations. , 2001, Journal of molecular biology.
[19] L L Looger,et al. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. , 2001, Journal of molecular biology.
[20] Thomas Bäck,et al. Evolutionary computation: Toward a new philosophy of machine intelligence , 1997, Complex..
[21] David B. Fogel,et al. Evolutionary algorithms in theory and practice , 1997, Complex.
[22] Gennady M Verkhivker,et al. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. , 1995, Chemistry & biology.
[23] J. Ponder,et al. Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.
[24] Pierre Tufféry,et al. A critical comparison of search algorithms applied to the optimization of protein side‐chain conformations , 1993, J. Comput. Chem..
[25] M. Levitt,et al. Protein folding: the endgame. , 1997, Annual review of biochemistry.
[26] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..
[27] I Lasters,et al. All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination. , 1997, Folding & design.
[28] C. Sander,et al. Fast and simple monte carlo algorithm for side chain optimization in proteins: Application to model building by homology , 1992, Proteins.
[29] Maximiliano Vásquez,et al. An evaluvation of discrete and continuum search techniques for conformational analysis of side chains in proteins , 1995 .
[30] David B. Fogel,et al. Evolutionary Computation: Towards a New Philosophy of Machine Intelligence , 1995 .
[31] A R Leach,et al. Exploring the conformational space of protein side chains using dead‐end elimination and the A* algorithm , 1998, Proteins.
[32] Roland L. Dunbrack,et al. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. , 1993, Journal of molecular biology.
[33] Roland L. Dunbrack,et al. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. , 1997, Journal of molecular biology.
[34] Cheng-Yan Kao,et al. Flexible ligand docking using a robust evolutionary algorithm , 2000, J. Comput. Chem..
[35] U. Singh,et al. A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .