Comparison of solvation‐effect methods for the simulation of peptide interactions with a hydrophobic surface
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[1] K. Kuczera,et al. Equilibrium structure and folding of a helix-forming peptide: circular dichroism measurements and replica-exchange molecular dynamics simulations. , 2004, Biophysical journal.
[2] Jeffry D. Madura,et al. A Brownian Dynamics Study of the Initial Stages of Hen Egg-White Lysozyme Adsorption at a Solid Interface , 2001 .
[3] Abraham Ulman,et al. Packing and Molecular Orientation of Alkanethiol Monolayers on Gold Surfaces , 1989 .
[4] Alexander D. MacKerell,et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.
[5] R. Tilton,et al. Spontaneous Reconfiguration of Adsorbed Lysozyme Layers Observed by Total Internal Reflection Fluorescence with a pH-Sensitive Fluorophore , 1996 .
[6] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[7] Jeffrey J. Gray,et al. The interaction of proteins with solid surfaces. , 2004, Current opinion in structural biology.
[8] Alexander D. MacKerell,et al. An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids , 2000 .
[9] Yu Sun,et al. Comparison of implicit solvent models for the simulation of protein–surface interactions , 2006, J. Comput. Chem..
[10] K. Dill,et al. Potential of mean force between two hydrophobic solutes in water. , 2002, Biophysical chemistry.
[11] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[12] 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.
[13] 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 .
[14] Johnson,et al. Adsorbed Layers of Ferritin at Solid and Fluid Interfaces Studied by Atomic Force Microscopy. , 2000, Journal of colloid and interface science.
[15] R. Misra,et al. Biomaterials , 2008 .
[16] Robert A. Latour,et al. Adsorption Thermodynamics Of A Mid-Chain Peptide Residue On Functionalized SAM Surfaces Using SPR , 2005 .
[17] M. Klein,et al. Molecular dynamics simulations of a protein on hydrophobic and hydrophilic surfaces. , 1996, Biophysical journal.
[18] J S Sharp,et al. Surface denaturation and amyloid fibril formation of insulin at model lipid-water interfaces. , 2002, Biochemistry.
[19] C. Brooks,et al. Novel generalized Born methods , 2002 .
[20] 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.
[21] A. Baumketner,et al. Free energy landscapes for amyloidogenic tetrapeptides dimerization. , 2005, Biophysical journal.
[22] H. Tsao,et al. Strong repulsive forces between protein and oligo (ethylene glycol) self-assembled monolayers: a molecular simulation study. , 2005, Biophysical journal.
[23] M. Karplus,et al. A Comprehensive Analytical Treatment of Continuum Electrostatics , 1996 .
[24] C. Brooks,et al. Recent advances in the development and application of implicit solvent models in biomolecule simulations. , 2004, Current opinion in structural biology.
[25] Robert A. Latour,et al. Theoretical analysis of adsorption thermodynamics for hydrophobic peptide residues on SAM surfaces of varying functionality , 2002 .
[26] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[27] Mihaly Mezei,et al. The Potentials of Mean Force of Sodium Chloride and Sodium Dimethylphosphate in Water : An Application of Adaptive Umbrella Sampling , 1995 .
[28] Seishi Shimizu,et al. Anti‐cooperativity and cooperativity in hydrophobic interactions: Three‐body free energy landscapes and comparison with implicit‐solvent potential functions for proteins , 2002, Proteins.
[29] P. J. Steinbach,et al. Exploring peptide energy landscapes: A test of force fields and implicit solvent models , 2004, Proteins.
[30] Bernard Sebille,et al. Modeling of Protein Adsorption on Polymer Surfaces. Computation of Adsorption Potential , 1995 .
[31] Christian Bartels,et al. Solution conformations of structured peptides: continuum electrostatics versus distance-dependent dielectric functions , 1999 .
[32] T. Lazaridis,et al. Potentials of mean force between ionizable amino acid side chains in water. , 2003, Journal of the American Chemical Society.
[33] B. Roux. The calculation of the potential of mean force using computer simulations , 1995 .
[34] F. Young. Biochemistry , 1955, The Indian Medical Gazette.
[35] W. V. Gunsteren,et al. The elucidation of enzymatic reaction mechanisms by computer simulation: Human immunodeficiency virus protease catalysis , 1998 .
[36] A. Liwo,et al. Molecular simulation study of cooperativity in hydrophobic association: clusters of four hydrophobic particles. , 2003, Biophysical chemistry.
[37] Larry L Hench,et al. A theoretical analysis of the thermodynamic contributions for the adsorption of individual protein residues on functionalized surfaces. , 2002, Biomaterials.
[38] Robert A Latour,et al. Molecular dynamics simulations of peptide-surface interactions. , 2005, Langmuir : the ACS journal of surfaces and colloids.