Comparison of implicit solvent models for the simulation of protein–surface interactions
暂无分享,去创建一个
[1] J. R. Long,et al. Structure and dynamics of hydrated statherin on hydroxyapatite as determined by solid-state NMR. , 2001, Biochemistry.
[2] C. Brooks,et al. Recent advances in the development and application of implicit solvent models in biomolecule simulations. , 2004, Current opinion in structural biology.
[3] Shaoyi Jiang,et al. Molecular simulation study of water interactions with oligo (ethylene glycol)-terminated alkanethiol self-assembled monolayers. , 2004, Langmuir : the ACS journal of surfaces and colloids.
[4] A. Vermeer,et al. Structural changes of IgG induced by heat treatment and by adsorption onto a hydrophobic Teflon surface studied by circular dichroism spectroscopy. , 1998, Biochimica et biophysica acta.
[5] G. Somorjai,et al. Molecular packing of lysozyme, fibrinogen, and bovine serum albumin on hydrophilic and hydrophobic surfaces studied by infrared-visible sum frequency generation and fluorescence microscopy. , 2003, Journal of the American Chemical Society.
[6] Stephen E. Creager,et al. Contact-Angle Titrations of Mixed .omega.-Mercaptoalkanoic Acid/Alkanethiol Monolayers on Gold. Reactive vs Nonreactive Spreading, and Chain Length Effects on Surface pKa Values , 1994 .
[7] Clayton J. Radke,et al. Direct Imaging of Lysozyme Adsorption onto Mica by Atomic Force Microscopy , 2002 .
[8] K. Dill,et al. A View of the Hydrophobic Effect , 2002 .
[9] B Honig,et al. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. , 1991, Science.
[10] Robert A Latour,et al. Molecular dynamics simulations of peptide-surface interactions. , 2005, Langmuir : the ACS journal of surfaces and colloids.
[11] Shaoyi Jiang,et al. Strong resistance of phosphorylcholine self-assembled monolayers to protein adsorption: insights into nonfouling properties of zwitterionic materials. , 2005, Journal of the American Chemical Society.
[12] Abraham Ulman,et al. Packing and Molecular Orientation of Alkanethiol Monolayers on Gold Surfaces , 1989 .
[13] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[14] Bernard Sebille,et al. Modeling of Protein Adsorption on Polymer Surfaces. Computation of Adsorption Potential , 1995 .
[15] Christian Bartels,et al. Solution conformations of structured peptides: continuum electrostatics versus distance-dependent dielectric functions , 1999 .
[16] T. Lazaridis,et al. Potentials of mean force between ionizable amino acid side chains in water. , 2003, Journal of the American Chemical Society.
[17] F. Young. Biochemistry , 1955, The Indian Medical Gazette.
[18] Jeffrey J. Gray,et al. The interaction of proteins with solid surfaces. , 2004, Current opinion in structural biology.
[19] Alexander D. MacKerell,et al. An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids , 2000 .
[20] Sylvie Le Borgne,et al. Biotechnological processes for the refining of petroleum , 2003 .
[21] Robert A. Latour,et al. Theoretical analysis of adsorption thermodynamics for hydrophobic peptide residues on SAM surfaces of varying functionality , 2002 .
[22] Fabio Ganazzoli,et al. Simulation study of the interaction of some albumin subdomains with a flat graphite surface , 2003 .
[23] Sergey A. Piletsky,et al. Application of natural receptors in sensors and assays. , 2002, Analytical chemistry.
[24] M. Karplus,et al. Effective energy function for proteins in solution , 1999, Proteins.
[25] A. D. McLachlan,et al. Solvation energy in protein folding and binding , 1986, Nature.
[26] Daniel Forciniti,et al. Monte Carlo simulations of peptide adsorption on solid surfaces (Monte Carlo simulations of peptide adsorption) , 2001 .
[27] Robert A. Latour,et al. Molecular modeling of biomaterial surfaces , 1999 .
[28] W. Norde,et al. Influence of hydrophobic Teflon particles on the structure of amyloid beta-peptide. , 2003, Biomacromolecules.
[29] W. C. Still,et al. Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .
[30] J S Sharp,et al. Surface denaturation and amyloid fibril formation of insulin at model lipid-water interfaces. , 2002, Biochemistry.
[31] T. Simonson,et al. Protein molecular dynamics with the generalized born/ACE solvent model , 2001, Proteins.
[32] D. Eisenberg,et al. Atomic solvation parameters applied to molecular dynamics of proteins in solution , 1992, Protein science : a publication of the Protein Society.
[33] J. Valverde. Molecular Modelling: Principles and Applications , 2001 .
[34] A. Goldstein,et al. Effect of adsorbed fibronectin concentration on cell adhesion and deformation under shear on hydrophobic surfaces. , 2002, Journal of biomedical materials research.
[35] Robert A. Latour,et al. Adsorption Thermodynamics Of A Mid-Chain Peptide Residue On Functionalized SAM Surfaces Using SPR , 2005 .
[36] Abraham M. Lenhoff,et al. Influence of Structural Details in Modeling Electrostatically Driven Protein Adsorption , 1997 .
[37] P. Privalov,et al. Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration. , 1993, Journal of molecular biology.
[38] A. Leach. Molecular Modelling: Principles and Applications , 1996 .
[39] Fabio Ganazzoli,et al. Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface. , 2004, Langmuir : the ACS journal of surfaces and colloids.
[40] R. Misra,et al. Biomaterials , 2008 .
[41] Charles A Haynes,et al. Mesoscopic dynamic Monte Carlo simulations of the adsorption of proteinlike HP chains within laterally constricted spaces. , 2005, Journal of colloid and interface science.
[42] Larry L Hench,et al. A theoretical analysis of the thermodynamic contributions for the adsorption of individual protein residues on functionalized surfaces. , 2002, Biomaterials.
[43] M. Karplus,et al. A Comprehensive Analytical Treatment of Continuum Electrostatics , 1996 .
[44] Johnson,et al. Adsorbed Layers of Ferritin at Solid and Fluid Interfaces Studied by Atomic Force Microscopy. , 2000, Journal of colloid and interface science.
[45] K. Park,et al. Calculation of solvation interaction energies for protein adsorption on polymer surfaces. , 1991, Journal of biomaterials science. Polymer edition.
[46] B. Honig,et al. New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects , 1996 .
[47] Stephen R. Euston,et al. Computer simulation of proteins: adsorption, gelation and self-association , 2004 .
[48] M. Klein,et al. Molecular dynamics simulations of a protein on hydrophobic and hydrophilic surfaces. , 1996, Biophysical journal.
[49] Joel J. P. C. Rodrigues,et al. Fuel Process. Technol. , 2005 .
[50] Shaoyi Jiang,et al. Monte Carlo simulations of antibody adsorption and orientation on charged surfaces. , 2004, The Journal of chemical physics.
[51] A. Lenhoff,et al. Analysis of ordered arrays of adsorbed lysozyme by scanning tunneling microscopy. , 1993, Biophysical journal.
[52] Kinam Park,et al. Protein interaction with surfaces: Separation distance‐dependent interaction energies , 1994 .
[53] Elazer R Edelman,et al. Effect of pre‐adsorbed proteins on attachment, proliferation, and function of endothelial cells , 2002, Journal of cellular physiology.
[54] R. Tilton,et al. Spontaneous Reconfiguration of Adsorbed Lysozyme Layers Observed by Total Internal Reflection Fluorescence with a pH-Sensitive Fluorophore , 1996 .
[55] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[56] P. Sridhar,et al. Design of affinity membrane bioseparations , 1996 .
[57] Fredrik Carlsson,et al. Lysozyme adsorption to charged surfaces : A Monte Carlo Study , 2004 .
[58] B. Honig,et al. Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory , 1994 .
[59] Paul R Van Tassel,et al. Surface-induced conformational changes in lattice model proteins by Monte Carlo simulation. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.
[60] Xin Xu,et al. From The Cover: The X3LYP extended density functional for accurate descriptions of nonbond interactions, spin states, and thermochemical properties. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[61] W. Pitt,et al. Water structure around enkephalin near a GeO2 surface: a molecular dynamics study. , 2002, Journal of biomaterials science. Polymer edition.
[62] Jeffry D. Madura,et al. A Brownian Dynamics Study of the Initial Stages of Hen Egg-White Lysozyme Adsorption at a Solid Interface , 2001 .
[63] Brian J. Teppen,et al. Molecular dynamics simulations of the adsorption of proteins on clay mineral surfaces , 2000 .
[64] Frank Caruso,et al. Preparation of enzyme multilayers on colloids for biocatalysis , 2000 .
[65] Robert A Latour,et al. Molecular simulation to characterize the adsorption behavior of a fibrinogen gamma-chain fragment. , 2005, Langmuir : the ACS journal of surfaces and colloids.
[66] Shaoyi Jiang,et al. Molecular Simulation Studies of the Orientation and Conformation of Cytochrome c Adsorbed on Self-Assembled Monolayers , 2004 .
[67] George M. Whitesides,et al. Adsorption of Proteins to Hydrophobic Sites on Mixed Self-Assembled Monolayers† , 2003 .
[68] K. Park,et al. Protein adsorption on polymer surfaces: calculation of adsorption energies. , 1990, Journal of biomaterials science. Polymer edition.
[69] M. Karplus,et al. Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation model. , 1998, Journal of molecular biology.