A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models
暂无分享,去创建一个
Alessandra Villa | Christine Peter | Mehmet Sayar | C. Peter | A. Villa | M. Sayar | Ozge Engin | O. Engin
[1] Gregory C Rutledge,et al. A novel algorithm for creating coarse-grained, density dependent implicit solvent models. , 2008, The Journal of chemical physics.
[2] Gregory A Voth,et al. The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures. , 2009, The Journal of chemical physics.
[3] D Thirumalai,et al. The nature of folded states of globular proteins , 1992, Biopolymers.
[4] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[5] Y. Levi-Kalisman,et al. Matrices of Acidic β‐Sheet Peptides as Templates for Calcium Phosphate Mineralization , 2008 .
[6] Alessandra Villa,et al. Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation. , 2009, Physical chemistry chemical physics : PCCP.
[7] Alessandra Villa,et al. Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model. , 2009, Physical chemistry chemical physics : PCCP.
[8] Lanyuan Lu,et al. Multiscale Coarse-Graining of the Protein Energy Landscape , 2010, PLoS Comput. Biol..
[9] Cecilia Clementi,et al. Coarse-grained models of protein folding: toy models or predictive tools? , 2008, Current opinion in structural biology.
[10] H. Matsui,et al. Peptide‐Based Nanotubes and Their Applications in Bionanotechnology , 2005, Advanced materials.
[11] Tristan Bereau,et al. Generic coarse-grained model for protein folding and aggregation. , 2009, The Journal of chemical physics.
[12] Siewert J Marrink,et al. Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. , 2011, Physical chemistry chemical physics : PCCP.
[13] Ehud Gazit,et al. Peptide self-assembly at the nanoscale: a challenging target for computational and experimental biotechnology. , 2007, Trends in biotechnology.
[14] Kurt Kremer,et al. Tunable generic model for fluid bilayer membranes. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.
[15] 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.
[16] A. Liwo,et al. A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: Application to the UNRES force field , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[17] William George Noid,et al. Extended ensemble approach for deriving transferable coarse-grained potentials , 2009 .
[18] Ruth Nussinov,et al. Coarse-grained representation of β-helical protein building blocks , 2007 .
[19] Joan-Emma Shea,et al. Self-assembly of β-sheet forming peptides into chiral fibrillar aggregates , 2007 .
[20] Florian Müller-Plathe,et al. Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back. , 2002, Chemphyschem : a European journal of chemical physics and physical chemistry.
[21] Gregory A Voth,et al. A multiscale coarse-graining method for biomolecular systems. , 2005, The journal of physical chemistry. B.
[22] R. Jernigan,et al. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation , 1985 .
[23] Michael L Klein,et al. Understanding nature's design for a nanosyringe. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[24] Kurt Kremer,et al. Simulation of polymer melts. I. Coarse‐graining procedure for polycarbonates , 1998 .
[25] Wilfred F van Gunsteren,et al. Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. , 2007, Chemphyschem : a European journal of chemical physics and physical chemistry.
[26] Normand Mousseau,et al. Coarse-grained protein molecular dynamics simulations. , 2007, The Journal of chemical physics.
[27] Berk Hess,et al. Modeling multibody effects in ionic solutions with a concentration dependent dielectric permittivity. , 2006, Physical review letters.
[28] Gregory A Voth,et al. Multiscale modeling of biomolecular systems: in serial and in parallel. , 2007, Current opinion in structural biology.
[29] Kurt Kremer,et al. Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back , 2009 .
[30] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[31] Kurt Kremer,et al. Comparison between coarse-graining models for polymer systems: Two mapping schemes for polystyrene , 2007 .
[32] Peter J Bond,et al. Insertion and assembly of membrane proteins via simulation. , 2006, Journal of the American Chemical Society.
[33] Wataru Shinoda,et al. Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants , 2007 .
[34] John G. Curro,et al. Mapping of Explicit Atom onto United Atom Potentials , 1998 .
[35] Florian Müller-Plathe,et al. Multicentered Gaussian‐based potentials for coarse‐grained polymer simulations: Linking atomistic and mesoscopic scales , 2005 .
[36] Ilpo Vattulainen,et al. Multiscale modeling of emergent materials: biological and soft matter. , 2009, Physical chemistry chemical physics : PCCP.
[37] E. Gazit. Mechanisms of amyloid fibril self‐assembly and inhibition , 2005, The FEBS journal.
[38] Yundong Wu,et al. Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model: Molecular Dynamics Study of Polyalanine-Based Peptides. , 2007, Journal of chemical theory and computation.
[39] S. Stupp,et al. Branched peptide-amphiphiles as self-assembling coatings for tissue engineering scaffolds. , 2006, Journal of biomedical materials research. Part A.
[40] C. Hall,et al. Phase diagrams describing fibrillization by polyalanine peptides. , 2004, Biophysical journal.
[41] Michele Cascella,et al. A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements. , 2010, Journal of chemical theory and computation.
[42] 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.
[43] Wataru Shinoda,et al. A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids. , 2009, Journal of chemical theory and computation.
[44] G. Schatz,et al. Modeling self-assembly processes driven by nonbonded interactions in soft materials. , 2008, The journal of physical chemistry. B.
[45] Attila Szolnoki,et al. Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions , 2010, PLoS Comput. Biol..
[46] Gregory A. Voth,et al. The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. , 2008, The Journal of chemical physics.
[47] R. Larson,et al. The MARTINI Coarse-Grained Force Field: Extension to Proteins. , 2008, Journal of chemical theory and computation.
[48] George M. Whitesides,et al. Beyond molecules: Self-assembly of mesoscopic and macroscopic components , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[49] Kurt Kremer,et al. Coarse-Grained Polymer Melts Based on Isolated Atomistic Chains: Simulation of Polystyrene of Different Tacticities , 2009 .
[50] R. C. Reeder,et al. A Coarse Grain Model for Phospholipid Simulations , 2001 .
[51] J Andrew McCammon,et al. Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model. , 2006, Journal of chemical theory and computation.
[52] Carl Henrik Görbitz,et al. Microporous organic materials from hydrophobic dipeptides. , 2007, Chemistry.
[53] Gregory C Rutledge,et al. Evaluating the transferability of coarse-grained, density-dependent implicit solvent models to mixtures and chains. , 2009, The Journal of chemical physics.
[54] Daniel Borgis,et al. A coarse-grained protein-protein potential derived from an all-atom force field. , 2007, The journal of physical chemistry. B.
[55] Jan Fischer,et al. Modeling of aqueous poly(oxyethylene) solutions. 2. Mesoscale simulations. , 2008, The journal of physical chemistry. B.
[56] Margaret E. Johnson,et al. Representability problems for coarse-grained water potentials. , 2007, The Journal of chemical physics.
[57] 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.
[58] Jim Pfaendtner,et al. A systematic methodology for defining coarse-grained sites in large biomolecules. , 2008, Biophysical journal.
[59] M. Ghadiri,et al. Peptide Nanotubes and Beyond , 1998 .
[60] Kurt Kremer,et al. Combined Coarse-Grained and Atomistic Simulation of Liquid Bisphenol A-Polycarbonate: Liquid Packing and Intramolecular Structure , 2003 .
[61] Kurt Kremer,et al. Effects of excluded volume and bond length on the dynamics of dense bead-spring polymer melts , 2002 .
[62] Kurt Kremer,et al. Hierarchical modeling of polystyrene: From atomistic to coarse-grained simulations , 2006 .
[63] Michael L. Klein,et al. A coarse grain model for n-alkanes parameterized from surface tension data , 2003 .
[64] Gregory A Voth,et al. Multiscale coarse-graining and structural correlations: connections to liquid-state theory. , 2007, The journal of physical chemistry. B.
[65] P. Derreumaux,et al. A coarse‐grained protein force field for folding and structure prediction , 2007, Proteins.
[66] T. Holmes,et al. Novel peptide-based biomaterial scaffolds for tissue engineering. , 2002, Trends in biotechnology.
[67] Tap Ha-Duong,et al. Protein Backbone Dynamics Simulations Using Coarse-Grained Bonded Potentials and Simplified Hydrogen Bonds. , 2010, Journal of chemical theory and computation.
[68] R. Weissleder,et al. Peptide-based biomaterials for protease-enhanced drug delivery. , 2006, Biomacromolecules.
[69] Wataru Shinoda,et al. Coarse-grained potential models for phenyl-based molecules: I. Parametrization using experimental data. , 2010, The journal of physical chemistry. B.
[70] D. Altschuh,et al. A peptide-based, ratiometric biosensor construct for direct fluorescence detection of a protein analyte. , 2008, Bioconjugate chemistry.
[71] Alessandra Villa,et al. Transferability of Nonbonded Interaction Potentials for Coarse-Grained Simulations: Benzene in Water. , 2010, Journal of chemical theory and computation.
[72] 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.
[73] Alexander J. Marchut,et al. Solvent effects on the conformational transition of a model polyalanine peptide , 2004, Protein science : a publication of the Protein Society.
[74] C. Hall,et al. Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[75] Henry Bock,et al. Mesoscale modeling of complex binary fluid mixtures: towards an atomistic foundation of effective potentials. , 2006, The Journal of chemical physics.
[76] Cecilia Clementi,et al. Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[77] Gregory A Voth,et al. Coarse-grained peptide modeling using a systematic multiscale approach. , 2007, Biophysical journal.
[78] Berk Hess,et al. Osmotic coefficients of atomistic NaCl (aq) force fields. , 2006, The Journal of chemical physics.
[79] Sang-Jin Suh,et al. Recent advances in peptide probe-based biosensors for detection of infectious agents. , 2009, Journal of microbiological methods.
[80] Thomas M Truskett,et al. Coarse-grained strategy for modeling protein stability in concentrated solutions. , 2005, Biophysical journal.
[81] B. Maigret,et al. Self assembly of peptides near or within membranes using coarse grained MD simulations , 2009 .
[82] A. Liwo,et al. A united‐residue force field for off‐lattice protein‐structure simulations. I. Functional forms and parameters of long‐range side‐chain interaction potentials from protein crystal data , 1997 .
[83] P. Wolynes,et al. Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer , 1999 .
[84] Kurt Kremer,et al. Classical simulations from the atomistic to the mesoscale and back: coarse graining an liquid crystal. , 2008, Soft matter.
[85] K. Binder,et al. Coarse-grained models for fluids and their mixtures: Comparison of Monte Carlo studies of their phase behavior with perturbation theory and experiment. , 2008, The Journal of chemical physics.
[86] Alexander Lukyanov,et al. Versatile Object-Oriented Toolkit for Coarse-Graining Applications. , 2009, Journal of chemical theory and computation.
[87] D. Tieleman,et al. The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.
[88] Julien Michel,et al. Prediction of partition coefficients by multiscale hybrid atomic-level/coarse-grain simulations. , 2008, The journal of physical chemistry. B.
[89] A. Mark,et al. Coarse grained model for semiquantitative lipid simulations , 2004 .
[90] Ilpo Vattulainen,et al. Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer. , 2009, The Journal of chemical physics.