An implicit solvent coarse-grained lipid model with correct stress profile.
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[1] D. J. Tildesley,et al. The shape dependence of the solute-solvent interactions in a liquid crystalline phase: A computer simulation study. , 1996 .
[2] E. Lieb,et al. The inverse problem in classical statistical mechanics , 1984 .
[3] Teresa Head-Gordon,et al. Protein Engineering Study of Protein L by Simulation , 2002, J. Comput. Biol..
[4] Ilpo Vattulainen,et al. Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints. , 2007, The Journal of chemical physics.
[5] M. Patra,et al. Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. , 2003, Biophysical journal.
[6] Jeffery B. Klauda,et al. Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers. , 2008, The journal of physical chemistry. B.
[7] E. Lindahl,et al. Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations , 2000 .
[8] D Thirumalai,et al. Factors governing the foldability of proteins , 1996, Proteins.
[9] R. Clegg,et al. Translational diffusion of lipids in liquid crystalline phase phosphatidylcholine multibilayers. A comparison of experiment with theory. , 1985, Biochemistry.
[10] I. Vattulainen,et al. Polyunsaturation in lipid membranes: dynamic properties and lateral pressure profiles. , 2007, The journal of physical chemistry. B.
[11] D. Marsh,et al. Elastic curvature constants of lipid monolayers and bilayers. , 2006, Chemistry and physics of lipids.
[12] J. Sorenson,et al. Toward minimalist models of larger proteins: A ubiquitin‐like protein , 2002, Proteins.
[13] Jonathan W Essex,et al. A quantitative coarse-grain model for lipid bilayers. , 2008, The journal of physical chemistry. B.
[14] Kurt Kremer,et al. Tunable generic model for fluid bilayer membranes. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.
[15] R. L. Henderson. A uniqueness theorem for fluid pair correlation functions , 1974 .
[16] A. Lyubartsev,et al. Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach. , 1995, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[17] Grace Brannigan,et al. Flexible lipid bilayers in implicit solvent. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.
[18] Berend Smit,et al. Mesoscopic models of biological membranes , 2006 .
[19] Richard H. Templer,et al. Modulation of folding and assembly of the membrane protein bacteriorhodopsin by intermolecular forces within the lipid bilayer. , 1999 .
[20] A. Menon,et al. Lipid flippases and their biological functions , 2006, Cellular and Molecular Life Sciences CMLS.
[21] H. C. Andersen. Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations , 1983 .
[22] B. Smit,et al. Comparison of mesoscopic phospholipid-water models , 2004 .
[23] Gregory A Voth,et al. Solvent-free lipid bilayer model using multiscale coarse-graining. , 2009, The journal of physical chemistry. B.
[24] J. Henderson,et al. Statistical mechanics of inhomogeneous fluids , 1982, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.
[25] R. D. Groot,et al. Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants. , 2001, Biophysical journal.
[26] Berend Smit,et al. Simulation studies of protein-induced bilayer deformations, and lipid-induced protein tilting, on a mesoscopic model for lipid bilayers with embedded proteins. , 2005, Biophysical journal.
[27] J. Onuchic,et al. Prediction of folding mechanism for circular-permuted proteins. , 2001, Journal of molecular biology.
[28] Dirk Reith,et al. Deriving effective mesoscale potentials from atomistic simulations , 2002, J. Comput. Chem..
[29] Teresa Head-Gordon,et al. Matching simulation and experiment (extended abstract): a new simplified model for simulating protein folding , 2000, RECOMB '00.
[30] M. Cieplak,et al. Scaling of Folding Properties in Simple Models of Proteins , 1999, cond-mat/9907269.
[31] Oded Farago,et al. Mode excitation Monte Carlo simulations of mesoscopically large membranes. , 2008, The Journal of chemical physics.
[32] T. Head-Gordon,et al. Intermediates and the folding of proteins L and G , 2004, Protein science : a publication of the Protein Society.
[33] H. C. Andersen,et al. Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids , 1971 .
[34] Alexander D. MacKerell,et al. An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. , 2005, The journal of physical chemistry. B.
[35] K. Kohlstedt,et al. Contrasting disease and nondisease protein aggregation by molecular simulation. , 2008, Accounts of chemical research.
[36] O. Farago. “Water-free” computer model for fluid bilayer membranes , 2003, cond-mat/0304203.
[37] Hiroshi Noguchi,et al. Fluid vesicles with viscous membranes in shear flow. , 2004, Physical review letters.
[38] Klaus Schulten,et al. Lipid bilayer pressure profiles and mechanosensitive channel gating. , 2004, Biophysical journal.
[39] R. Templer,et al. Sensing isothermal changes in the lateral pressure in model membranes using di-pyrenyl phosphatidylcholine. , 1998, Faraday discussions.
[40] D. Tieleman,et al. The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.
[41] Roland Faller,et al. Coarse-grained modeling of lipids. , 2009, Chemistry and physics of lipids.
[42] A. Mark,et al. Coarse grained model for semiquantitative lipid simulations , 2004 .
[43] Ilpo Vattulainen,et al. Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer. , 2009, The Journal of chemical physics.
[44] C L Brooks,et al. Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[45] Ole G Mouritsen,et al. Artifacts in dynamical simulations of coarse-grained model lipid bilayers. , 2005, The Journal of chemical physics.
[46] R. Kornberg,et al. Inside-outside transitions of phospholipids in vesicle membranes. , 1971, Biochemistry.
[47] O. Farago,et al. Statistical mechanics of bilayer membrane with a fixed projected area. , 2003, The Journal of chemical physics.
[48] Scott Brown,et al. Influence of denatured and intermediate states of folding on protein aggregation , 2005, Protein science : a publication of the Protein Society.
[49] J. Onuchic,et al. Theory of protein folding: the energy landscape perspective. , 1997, Annual review of physical chemistry.
[50] Frank L. H. Brown,et al. Implicit solvent simulation models for biomembranes , 2005, European Biophysics Journal.
[51] A. Kolb,et al. Optimized Constant Pressure Stochastic Dynamics , 1999 .
[52] Scott Brown,et al. Coarse-grained sequences for protein folding and design , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[53] W. Helfrich. Elastic Properties of Lipid Bilayers: Theory and Possible Experiments , 1973, Zeitschrift fur Naturforschung. Teil C: Biochemie, Biophysik, Biologie, Virologie.
[54] L A Mirny,et al. How evolution makes proteins fold quickly. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[55] T. Head-Gordon,et al. Minimalist models for protein folding and design. , 2003, Current opinion in structural biology.
[56] S. Bezrukov. Functional consequences of lipid packing stress , 2000 .
[57] Daan Frenkel,et al. Modeling flexible amphiphilic bilayers: a solvent-free off-lattice Monte Carlo study. , 2005, The Journal of chemical physics.
[58] Florian Müller-Plathe,et al. Mapping atomistic simulations to mesoscopic models: a systematic coarse-graining procedure for vinyl polymer chains. , 2005, The journal of physical chemistry. B.
[59] K. Dill,et al. From Levinthal to pathways to funnels , 1997, Nature Structural Biology.
[60] D Peter Tieleman,et al. Lipids out of equilibrium: energetics of desorption and pore mediated flip-flop. , 2006, Journal of the American Chemical Society.
[61] A C Maggs,et al. Computer simulations of self-assembled membranes. , 1991, Science.
[62] Reinhard Lipowsky,et al. Computer simulations of bilayer membranes - self-assembly and interfacial tension. , 1998 .
[63] J. Nagle,et al. Structure of lipid bilayers. , 2000, Biochimica et biophysica acta.
[64] E. Sackmann,et al. Neutron Spin Echo Study of Membrane Undulations in Lipid Multibilayers , 1993 .
[65] Solvent-free model for self-assembling fluid bilayer membranes: stabilization of the fluid phase based on broad attractive tail potentials. , 2005, The Journal of chemical physics.
[66] P. Canham. The minimum energy of bending as a possible explanation of the biconcave shape of the human red blood cell. , 1970, Journal of theoretical biology.
[67] Jennifer Chayes,et al. On the validity of the inverse conjecture in classical density functional theory , 1984 .
[68] A rigorous procedure for combining molecular dynamics and Monte Carlo simulation algorithms , 2000 .