De Novo Protein Folding with Distributed Computational Resources
暂无分享,去创建一个
Abhinav Verma | Wolfgang Wenzel | Alexander Schug | Timo Strunk | Konstantin V. Klenin | Srinivasa M. Gopal | K. Klenin | A. Schug | A. Verma | W. Wenzel | S. M. Gopal | T. Strunk
[1] A. Schug,et al. Energy landscape paving simulations of the trp-cage protein. , 2005, The Journal of chemical physics.
[2] J. Onuchic,et al. Theory of protein folding: the energy landscape perspective. , 1997, Annual review of physical chemistry.
[3] K. Dill,et al. A lattice statistical mechanics model of the conformational and sequence spaces of proteins , 1989 .
[4] C. Brooks,et al. From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. , 2001, Annual review of physical chemistry.
[5] Jeffrey C. Miller,et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases , 2005, Nature.
[6] P E Wright,et al. DNA-induced alpha-helix capping in conserved linker sequences is a determinant of binding affinity in Cys(2)-His(2) zinc fingers. , 2000, Journal of molecular biology.
[7] Karplus,et al. Protein folding bottlenecks: A lattice Monte Carlo simulation. , 1991, Physical review letters.
[8] P. Bolhuis,et al. Sampling the multiple folding mechanisms of Trp-cage in explicit solvent , 2006, Proceedings of the National Academy of Sciences.
[9] M J Sippl,et al. Knowledge-based potentials for proteins. , 1995, Current opinion in structural biology.
[10] Wolfgang Wenzel,et al. De novo Folding of Two-Helix Potassium Channel Blockers with Free-Energy Models and Molecular Dynamics. , 2007, Journal of chemical theory and computation.
[11] J. Doye,et al. Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms , 1997, cond-mat/9803344.
[12] J. W. Neidigh,et al. Designing a 20-residue protein , 2002, Nature Structural Biology.
[13] Wolfgang Wenzel,et al. A stochastic tunneling approach for global minimization , 1999 .
[14] A. Schug,et al. Reproducible protein folding with the stochastic tunneling method. , 2003, Physical review letters.
[15] G L Gilliland,et al. Structural studies of the engrailed homeodomain , 1994, Protein science : a publication of the Protein Society.
[16] S. Buldyrev,et al. Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model. , 2004, Biophysical journal.
[17] Abhinav Verma,et al. All‐atom de novo protein folding with a scalable evolutionary algorithm , 2007, J. Comput. Chem..
[18] Richard Bonneau,et al. Ab initio protein structure prediction: progress and prospects. , 2001, Annual review of biophysics and biomolecular structure.
[19] C. D. Gelatt,et al. Optimization by Simulated Annealing , 1983, Science.
[20] A. Sali,et al. Protein Structure Prediction and Structural Genomics , 2001, Science.
[21] Michal Sharon,et al. Alternative conformations of HIV-1 V3 loops mimic beta hairpins in chemokines, suggesting a mechanism for coreceptor selectivity. , 2003, Structure.
[22] Chin-Kun Hu,et al. Free energy landscape and folding mechanism of a β‐hairpin in explicit water: A replica exchange molecular dynamics study , 2005, Proteins.
[23] Wolfgang Wenzel,et al. Predictive in silico all-atom folding of a four-helix protein with a free-energy model. , 2004, Journal of the American Chemical Society.
[24] P. Wright,et al. Zinc finger proteins: new insights into structural and functional diversity. , 2001, Current opinion in structural biology.
[25] H. Scheraga,et al. Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H...O = C hydrogen bonds from packing configurations , 1984 .
[26] C. Branden,et al. Introduction to protein structure , 1991 .
[27] A. Schug,et al. All‐atom folding of the three‐helix HIV accessory protein with an adaptive parallel tempering method , 2004, Proteins.
[28] Valerie Daggett,et al. The complete folding pathway of a protein from nanoseconds to microseconds , 2003, Nature.
[29] M J Sippl,et al. Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. , 1992, Journal of molecular biology.
[30] D. Warrell,et al. Oxford textbook of medicine , 1983, The Ulster Medical Journal.
[31] F. Rao,et al. Replica exchange molecular dynamics simulations of reversible folding , 2003 .
[32] T. Hubbard,et al. Critical assessment of methods of protein structure prediction (CASP)‐round V , 2003, Proteins.
[33] V. Pande,et al. The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations. , 2002, Journal of the American Chemical Society.
[34] Wolfgang Wenzel,et al. Investigation of the parallel tempering method for protein folding , 2005 .
[35] Wolfgang Wenzel,et al. Protein structure prediction by all-atom free-energy refinement , 2006, BMC Structural Biology.
[36] S. Ishii,et al. Solution structure of the transactivation domain of ATF-2 comprising a zinc finger-like subdomain and a flexible subdomain. , 1999, Journal of molecular biology.
[37] Akbar Nayeem,et al. A comparative study of the simulated‐annealing and Monte Carlo‐with‐minimization approaches to the minimum‐energy structures of polypeptides: [Met]‐enkephalin , 1991 .
[38] Carl Branden,et al. The art of PS2 : the complete set of figures, panels and tables from introduction to protein structure , 1999 .
[39] A. Linhananta,et al. The equilibrium properties and folding kinetics of an all-atom Go model of the Trp-cage. , 2005, The Journal of chemical physics.
[40] L. Stryer,et al. Implications of X-ray crystallographic studies of protein structure. , 1968, Annual review of biochemistry.
[41] Wolfgang Wenzel,et al. Biomolecular Structure Prediction Stochastic Optimization Methods , 2005 .
[42] Wolfgang Wenzel,et al. Comparison of stochastic optimization methods for all-atom folding of the Trp-Cage protein. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.
[43] B. Rost. Review: protein secondary structure prediction continues to rise. , 2001, Journal of structural biology.
[44] A. Leach. Molecular Modelling: Principles and Applications , 1996 .
[45] W. Wenzel. Predictive folding of a β-hairpin protein in an all-atom free-energy model , 2006 .
[46] David J. Wales,et al. Energy landscapes, global optimization and dynamics of the polyalanine Ac(ala)8NHMe , 2001 .
[47] David J. Wales,et al. Energy landscapes of model polyalanines , 2002 .
[48] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[49] A. Schug,et al. Basin hopping simulations for all-atom protein folding. , 2006, The Journal of chemical physics.
[50] R. Abagyan,et al. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. , 1994, Journal of molecular biology.
[51] Zaida Luthey-Schulten,et al. Folding funnels: The key to robust protein structure prediction , 2002, J. Comput. Chem..
[52] D. Yee,et al. Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.
[53] K. Dill,et al. Protein folding in the landscape perspective: Chevron plots and non‐arrhenius kinetics , 1998, Proteins.
[54] Ruben Abagyan,et al. Ab InitioFolding of Peptides by the Optimal-Bias Monte Carlo Minimization Procedure , 1999 .
[55] N. Pavletich,et al. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A , 1991, Science.
[56] Wolfgang Wenzel,et al. De novo folding of the DNA-binding ATF-2 zinc finger motif in an all-atom free-energy forcefield. , 2006, Angewandte Chemie.
[57] David J Wales,et al. Effect of salt bridges on the energy landscape of a model protein. , 2004, The Journal of chemical physics.
[58] C. Pabo,et al. DNA recognition by Cys2His2 zinc finger proteins. , 2000, Annual review of biophysics and biomolecular structure.
[59] Harold A. Scheraga,et al. Analysis of the Contribution of Internal Vibrations to the Statistical Weights of Equilibrium Conformations of Macromolecules , 1969 .
[60] Giovanna Ghirlanda,et al. Membrane Proteins , 2013, Methods in Molecular Biology.
[61] W. Wenzel,et al. Scaling behavior of stochastic minimization algorithms in a perfect funnel landscape , 1999 .
[62] C. Dobson. The structural basis of protein folding and its links with human disease. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.
[63] Wolfgang Wenzel,et al. Massively Parallel All Atom Protein Folding in a Single Day , 2007, PARCO.
[64] V. Pande,et al. Multiplexed-replica exchange molecular dynamics method for protein folding simulation. , 2003, Biophysical journal.
[65] Julian Lee,et al. Folding of small proteins using a single continuous potential. , 2004, The Journal of chemical physics.
[66] J. M. Singer,et al. Bouncing towards the optimum: Improving the results of Monte Carlo optimization algorithms , 1998 .
[67] Valerie Daggett,et al. The present view of the mechanism of protein folding , 2003, Nature Reviews Molecular Cell Biology.
[68] Timothy F. Havel,et al. NMR structure determination in solution: a critique and comparison with X-ray crystallography. , 1992, Annual review of biophysics and biomolecular structure.
[69] N. Skelton,et al. Tryptophan zippers: Stable, monomeric β-hairpins , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[70] Stephen H White,et al. Membrane proteins--pumping along. , 2005, Current opinion in structural biology.
[71] P E Wright,et al. Three-dimensional solution structure of a single zinc finger DNA-binding domain. , 1989, Science.
[72] Wolfgang Wenzel,et al. Predictive and reproducible de novo all-atom folding of a β-hairpin loop in an improved free-energy forcefield , 2007 .
[73] F. Young. Biochemistry , 1955, The Indian Medical Gazette.