Generic coarse-grained model for protein folding and aggregation.
暂无分享,去创建一个
[1] Gregory A Voth,et al. Peptide folding using multiscale coarse-grained models. , 2008, The journal of physical chemistry. B.
[2] Bosco K. Ho,et al. Revisiting the Ramachandran plot: Hard‐sphere repulsion, electrostatics, and H‐bonding in the α‐helix , 2003, Protein science : a publication of the Protein Society.
[3] Alan M. Ferrenberg,et al. New Monte Carlo technique for studying phase transitions. , 1988, Physical review letters.
[4] C. Hall,et al. α‐Helix formation: Discontinuous molecular dynamics on an intermediate‐resolution protein model , 2001, Proteins.
[5] K. Schulten,et al. Calculating potentials of mean force from steered molecular dynamics simulations. , 2004, The Journal of chemical physics.
[6] J. Apostolakis,et al. Thermodynamics and Kinetics of Folding of Two Model Peptides Investigated by Molecular Dynamics Simulations , 2000 .
[7] A. Wand,et al. Structure of a de novo designed protein model of radical enzymes. , 2002, Journal of the American Chemical Society.
[8] Shankar Kumar,et al. Multidimensional free‐energy calculations using the weighted histogram analysis method , 1995, J. Comput. Chem..
[9] Birgit Schiøtt,et al. Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study. , 2008, Biophysical journal.
[10] Lydia E Kavraki,et al. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction , 2006, Proc. Natl. Acad. Sci. USA.
[11] Yinan Wei,et al. Solution structure of a de novo protein from a designed combinatorial library , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[12] B. Honig,et al. Free energy determinants of secondary structure formation: II. Antiparallel beta-sheets. , 1995, Journal of molecular biology.
[13] G. N. Ramachandran,et al. Stereochemistry of polypeptide chain configurations. , 1963, Journal of molecular biology.
[14] Alessandro Laio,et al. Reconstructing the density of states by history-dependent metadynamics. , 2004, Physical review letters.
[15] R. Jernigan,et al. An empirical energy potential with a reference state for protein fold and sequence recognition , 1999, Proteins.
[16] A. Godzik,et al. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? , 1997, Protein science : a publication of the Protein Society.
[17] Shoji Takada,et al. Optimizing physical energy functions for protein folding , 2003, Proteins.
[18] P. Wolynes,et al. Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer , 1999 .
[19] C. Pace,et al. Conformational stability of globular proteins. , 1990, Trends in biochemical sciences.
[20] Z. H. Wang,et al. Origin of the native driving force for protein folding. , 1999, Physical review letters.
[21] S. Gellman. Minimal model systems for β-sheet secondary structure in proteins , 1998 .
[22] C. Pace,et al. Forces contributing to the conformational stability of proteins , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.
[23] Joan-Emma Shea,et al. Self-assembly of β-sheet forming peptides into chiral fibrillar aggregates , 2007 .
[24] W. DeGrado,et al. Solution structure and dynamics of a de novo designed three-helix bundle protein. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[25] Margaret S. Cheung,et al. Mechanisms of cooperativity underlying sequence-independent β-sheet formation , 2001, cond-mat/0104065.
[26] L A Mirny,et al. How to derive a protein folding potential? A new approach to an old problem. , 1996, Journal of molecular biology.
[27] Hans-Jörg Limbach,et al. ESPResSo - an extensible simulation package for research on soft matter systems , 2006, Comput. Phys. Commun..
[28] N. Go. Theoretical studies of protein folding. , 1983, Annual review of biophysics and bioengineering.
[29] K. Dill,et al. A lattice statistical mechanics model of the conformational and sequence spaces of proteins , 1989 .
[30] Klaus Schulten,et al. Four-scale description of membrane sculpting by BAR domains. , 2008, Biophysical journal.
[31] Eng-Hui Yap,et al. Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abeta(1-40) peptide. , 2007, Journal of molecular biology.
[32] Dirk Reith,et al. Coarse Graining of Nonbonded Inter-Particle Potentials Using Automatic Simplex Optimization to Fit Structural Properties , 2000 .
[33] Eng‐Hui Yap,et al. A coarse‐grained α‐carbon protein model with anisotropic hydrogen‐bonding , 2008 .
[34] Robert H. Swendsen,et al. Optimized convergence for multiple histogram analysis , 2009, J. Comput. Phys..
[35] D. Hoffman,et al. Structure of the beta subunit of translation initiation factor 2 from the archaeon Methanococcus jannaschii: a representative of the eIF2beta/eIF5 family of proteins. , 2002, Biochemistry.
[36] H. Stanley,et al. Discrete molecular dynamics simulations of peptide aggregation. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.
[37] D. Thirumalai,et al. Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes , 2008, Protein science : a publication of the Protein Society.
[38] Wang,et al. Replica Monte Carlo simulation of spin glasses. , 1986, Physical review letters.
[39] M. Hecht,et al. Structure and dynamics of de novo proteins from a designed superfamily of 4‐helix bundles , 2008, Protein science : a publication of the Protein Society.
[40] Valentina Tozzini,et al. Coarse-grained models for proteins. , 2005, Current opinion in structural biology.
[41] R. Jernigan,et al. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. , 1996, Journal of molecular biology.
[42] Teresa Head-Gordon,et al. Matching simulation and experiment (extended abstract): a new simplified model for simulating protein folding , 2000, RECOMB '00.
[43] R. Larson,et al. The MARTINI Coarse-Grained Force Field: Extension to Proteins. , 2008, Journal of chemical theory and computation.
[44] G. Voth. Coarse-Graining of Condensed Phase and Biomolecular Systems , 2008 .
[45] Klaus Schulten,et al. Stability and dynamics of virus capsids described by coarse-grained modeling. , 2006, Structure.
[46] T. Head-Gordon,et al. Minimalist models for protein folding and design. , 2003, Current opinion in structural biology.
[47] J. Onuchic,et al. Folding kinetics of proteinlike heteropolymers , 1994, cond-mat/9404001.
[48] Gregory A Voth,et al. Multiscale modeling of biomolecular systems: in serial and in parallel. , 2007, Current opinion in structural biology.
[49] A. Irbäck,et al. Three-helix-bundle protein in a Ramachandran model. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[50] Nan-Yow Chen,et al. Effective potentials for folding proteins. , 2006, Physical review letters.
[51] A. Caflisch,et al. The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35 , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[52] P. Argos,et al. Knowledge‐based protein secondary structure assignment , 1995, Proteins.
[53] Yan Mu,et al. Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide. , 2007, The Journal of chemical physics.
[54] P. Lansbury,et al. A century-old debate on protein aggregation and neurodegeneration enters the clinic , 2006, Nature.
[55] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[56] J. Onuchic,et al. Funnels, pathways, and the energy landscape of protein folding: A synthesis , 1994, Proteins.
[57] Luis Serrano,et al. Combinatorial approaches: A new tool to search for highly structured β-hairpin peptides , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[58] Cecilia Clementi,et al. Minimalist protein model as a diagnostic tool for misfolding and aggregation. , 2006, Journal of molecular biology.
[59] S Subbiah,et al. Structure of the amino-terminal domain of phage 434 repressor at 2.0 A resolution. , 1989, Journal of molecular biology.
[60] G. Favrin,et al. Folding of a small helical protein using hydrogen bonds and hydrophobicity forces , 2001, Proteins: Structure, Function, and Bioinformatics.
[61] G. Torrie,et al. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .
[62] J. Onuchic,et al. Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[63] H. Lodish. Molecular Cell Biology , 1986 .
[64] R. Swendsen,et al. THE weighted histogram analysis method for free‐energy calculations on biomolecules. I. The method , 1992 .