Nonlinear vs. linear biasing in Trp-cage folding simulations.
暂无分享,去创建一个
[1] Massimiliano Bonomi,et al. Reconstructing the equilibrium Boltzmann distribution from well‐tempered metadynamics , 2009, J. Comput. Chem..
[2] W. C. Still,et al. The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii , 1997 .
[3] M. Parrinello,et al. From metadynamics to dynamics. , 2013, Physical review letters.
[4] Marino Arroyo,et al. Topological obstructions in the way of data-driven collective variables. , 2015, The Journal of chemical physics.
[5] Vojtěch Spiwok,et al. Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap. , 2011, The Journal of chemical physics.
[6] R. Dror,et al. How Fast-Folding Proteins Fold , 2011, Science.
[7] Vojtech Spiwok,et al. Metadynamics in essential coordinates: free energy simulation of conformational changes. , 2007, The journal of physical chemistry. B.
[8] H. Berendsen,et al. Essential dynamics of proteins , 1993, Proteins.
[9] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[10] Marino Arroyo,et al. Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables. , 2013, The Journal of chemical physics.
[11] J. Tenenbaum,et al. A global geometric framework for nonlinear dimensionality reduction. , 2000, Science.
[12] William Swope,et al. Understanding folding and design: Replica-exchange simulations of ``Trp-cage'' miniproteins , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[13] A. Laio,et al. Escaping free-energy minima , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[14] Francesco Luigi Gervasio,et al. From A to B in free energy space. , 2007, The Journal of chemical physics.
[15] M. Parrinello,et al. Well-tempered metadynamics: a smoothly converging and tunable free-energy method. , 2008, Physical review letters.
[16] A. Laio,et al. Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. , 2006, Journal of the American Chemical Society.
[17] Massimiliano Bonomi,et al. PLUMED: A portable plugin for free-energy calculations with molecular dynamics , 2009, Comput. Phys. Commun..
[18] Michele Parrinello,et al. Using sketch-map coordinates to analyze and bias molecular dynamics simulations , 2012, Proceedings of the National Academy of Sciences.
[19] P. Kollman,et al. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. , 1998, Science.
[20] J. W. Neidigh,et al. Designing a 20-residue protein , 2002, Nature Structural Biology.
[21] Shibasish Chowdhury,et al. Ab initio folding simulation of the Trp-cage mini-protein approaches NMR resolution. , 2003, Journal of molecular biology.
[22] M. Parrinello,et al. Canonical sampling through velocity rescaling. , 2007, The Journal of chemical physics.
[23] A. Laio,et al. Assessing the accuracy of metadynamics. , 2005, The journal of physical chemistry. B.
[24] Carsten Kutzner,et al. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.
[25] Lydia E Kavraki,et al. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction , 2006, Proc. Natl. Acad. Sci. USA.
[26] Francesco Luigi Gervasio,et al. Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin , 2010 .
[27] Vojtěch Spiwok,et al. Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes , 2008, Journal of molecular modeling.