Simulation of Peptide–Surface Recognition
暂无分享,去创建一个
[1] Ruth Pachter,et al. Nature of molecular interactions of peptides with gold, palladium, and Pd-Au bimetal surfaces in aqueous solution. , 2009, Journal of the American Chemical Society.
[2] S. Cannistraro,et al. A combined atomic force microscopy and molecular dynamics simulation study on a plastocyanin mutant chemisorbed on a gold surface. , 2003, Chemphyschem : a European journal of chemical physics and physical chemistry.
[3] S. Weiner,et al. Control and Design Principles in Biological Mineralization , 1992 .
[4] T. Xia,et al. Toxic Potential of Materials at the Nanolevel , 2006, Science.
[5] X. H. Wu,et al. Control of crystal phase switching and orientation by soluble mollusc-shell proteins , 1996, Nature.
[6] Ruth Pachter,et al. Toward understanding amino acid adsorption at metallic interfaces: a density functional theory study. , 2009, ACS applied materials & interfaces.
[7] Tiffany R. Walsh,et al. Modeling the Binding Affinity of Peptides for Graphitic Surfaces. Influences of Aromatic Content and Interfacial Shape , 2009 .
[8] Jeffry D. Madura,et al. A Brownian Dynamics Study of the Initial Stages of Hen Egg-White Lysozyme Adsorption at a Solid Interface , 2001 .
[9] K. Schulten,et al. Genetically engineered gold-binding polypeptides: structure prediction and molecular dynamics , 2002, Journal of biomaterials science. Polymer edition.
[10] Gennady M Verkhivker,et al. Towards understanding the mechanisms of molecular recognition by computer simulations of ligand–protein interactions , 1999, Journal of molecular recognition : JMR.
[11] Lucio Colombi Ciacchi,et al. A Classical Potential to Model the Adsorption of Biological Molecules on Oxidized Titanium Surfaces. , 2011, Journal of chemical theory and computation.
[12] Robert A Latour,et al. Correlation between desorption force measured by atomic force microscopy and adsorption free energy measured by surface plasmon resonance spectroscopy for peptide-surface interactions. , 2010, Langmuir : the ACS journal of surfaces and colloids.
[13] Ting Wang,et al. Protein–protein docking by simulating the process of association subject to biochemical constraints , 2008, Proteins.
[14] Jeffrey J. Gray,et al. De novo design of peptide-calcite biomineralization systems. , 2010, Journal of the American Chemical Society.
[15] J. Klein,et al. Large area, molecularly smooth (0.2 nm rms) gold films for surface forces and other studies. , 2007, Langmuir : the ACS journal of surfaces and colloids.
[16] L. Ghiringhelli,et al. Phenylalanine near inorganic surfaces: conformational statistics vs specific chemistry. , 2008, Journal of the American Chemical Society.
[17] R C Wade,et al. Electrostatic steering and ionic tethering in enzyme-ligand binding: insights from simulations. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[18] J. Garrido,et al. Peptide adsorption on a hydrophobic surface results from an interplay of solvation, surface, and intrapeptide forces , 2008, Proceedings of the National Academy of Sciences.
[19] M. Sternberg,et al. Prediction of protein-protein interactions by docking methods. , 2002, Current opinion in structural biology.
[20] M. W. Finnis,et al. The interaction of a point charge with an aluminium (111) surface , 1991 .
[21] N. Seeman,et al. Emulating biology: Building nanostructures from the bottom up , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[22] M. Grundmann,et al. Binding Specificity of a Peptide on Semiconductor Surfaces , 2004 .
[23] R. J. Green,et al. New insights on growth mechanisms of protein clusters at surfaces: an AFM and simulation study. , 2008, Langmuir : the ACS journal of surfaces and colloids.
[24] I. Cacelli,et al. Simulating DNA hybridization on an amine-functionalized silicon substrate. , 2010, The journal of physical chemistry. B.
[25] Stephen Mann,et al. Critical Transitions in the Biofabrication of Abalone Shells and Flat Pearls , 1996 .
[26] G. Truskey,et al. Effect of the conformation and orientation of adsorbed fibronectin on endothelial cell spreading and the strength of adhesion. , 1993, Journal of biomedical materials research.
[27] C. Hew,et al. Structure, function and evolution of antifreeze proteins , 1999, Cellular and Molecular Life Sciences CMLS.
[28] Stefano Corni,et al. Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces , 2008, J. Comput. Chem..
[29] Carlo Cavazzoni,et al. Hydroxyl-rich beta-sheet adhesion to the gold surface in water by first-principle simulations. , 2010, Journal of the American Chemical Society.
[30] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .
[31] M. Schrader. Wettability of clean metal surfaces , 1984 .
[32] Martin Hoefling,et al. ProMetCS: An Atomistic Force Field for Modeling Protein-Metal Surface Interactions in a Continuum Aqueous Solvent. , 2010, Journal of chemical theory and computation.
[33] J. J. Balbach,et al. Supramolecular Structure in Full-Length Alzheimer's β-Amyloid Fibrils: Evidence for a Parallel β-Sheet Organization from Solid-State Nuclear Magnetic Resonance , 2002 .
[34] Zongchao Jia,et al. Mimicry of ice structure by surface hydroxyls and water of a β-helix antifreeze protein , 2000, Nature.
[35] P. Ugliengo,et al. The role of defective silica surfaces in exogenous delivery of prebiotic compounds: clues from first principles calculations. , 2009, Physical chemistry chemical physics : PCCP.
[36] Jacqueline M Acres,et al. Investigating the specificity of peptide adsorption on gold using molecular dynamics simulations. , 2009, Biomacromolecules.
[37] Wolfhard Janke,et al. Microscopic mechanism of specific peptide adhesion to semiconductor substrates. , 2010, Angewandte Chemie.
[38] Stefano Corni,et al. Unraveling the Interaction between Histidine Side Chain and the Au(111) Surface : A DFT Study , 2008 .
[39] Tammy Nolan,et al. Ligand macromolecule interactions: theoretical principles of molecular recognition. , 2009, Methods in molecular biology.
[40] L. Addadi,et al. Monoclonal antibody recognition of cholesterol monohydrate crystal faces. , 1996, Chemistry & biology.
[41] P. Pyykkö,et al. Long-range interactions between polar molecules and metallic surfaces: A comparison of classical and density functional theory based models , 2009 .
[42] Eric A. Althoff,et al. De Novo Computational Design of Retro-Aldol Enzymes , 2008, Science.
[43] R C Wade,et al. Simulation of the diffusional association of barnase and barstar. , 1997, Biophysical journal.
[44] Martin Hoefling,et al. Interaction of amino acids with the Au(111) surface: adsorption free energies from molecular dynamics simulations. , 2010, Langmuir : the ACS journal of surfaces and colloids.
[45] U. Sivan,et al. A two-state electronic antigen and an antibody selected to discriminate between these states. , 2008, Nano letters.
[46] T. Walsh,et al. Interaction of liquid water with the rutile TiO2 (110) surface , 2007 .
[47] Richard A. Vaia,et al. Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12−6 and 9−6 Lennard-Jones Potentials , 2008 .
[48] S. Brown,et al. Engineered iron oxide-adhesion mutants of the Escherichia coli phage lambda receptor. , 1992, Proceedings of the National Academy of Sciences of the United States of America.
[49] J. Richardson,et al. Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[50] U. Sivan,et al. Antibody molecules discriminate between crystalline facets of a gallium arsenide semiconductor. , 2006, Nano letters.
[51] Luigi Delle Site,et al. Interaction of Hydrated Amino Acids with Metal Surfaces: A Multiscale Modeling Description , 2007 .
[52] K. West,et al. Differential adhesion of amino acids to inorganic surfaces , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[53] M. Payne,et al. Water structuring and collagen adsorption at hydrophilic and hydrophobic silicon surfaces. , 2009, Physical chemistry chemical physics : PCCP.
[54] M. Corno,et al. Ab initio modeling of protein/biomaterial interactions: competitive adsorption between glycine and water onto hydroxyapatite surfaces , 2009 .
[55] Gideon Schreiber,et al. Kinetic studies of protein-protein interactions. , 2002, Current opinion in structural biology.
[56] V. Mavrantzas,et al. Atomistic Simulation of Alkanethiol Self-Assembled Monolayers on Different Metal Surfaces via a Quantum, First-Principles Parametrization of the Sulfur−Metal Interaction , 2007, The Journal of Physical Chemistry C.
[57] Yu Sun,et al. Comparison of solvation‐effect methods for the simulation of peptide interactions with a hydrophobic surface , 2007, J. Comput. Chem..
[58] Albert Rimola,et al. Affinity Scale for the Interaction of Amino Acids with Silica Surfaces , 2009 .
[59] R C Wade,et al. Brownian dynamics simulation of protein-protein diffusional encounter. , 1998, Methods.
[60] J M Blaney,et al. A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.
[61] Berk Hess,et al. Competing adsorption between hydrated peptides and water onto metal surfaces: from electronic to conformational properties. , 2008, Journal of the American Chemical Society.
[62] Car,et al. Unified approach for molecular dynamics and density-functional theory. , 1985, Physical review letters.
[63] Robert A Latour,et al. Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review) , 2008, Biointerphases.
[64] S. Monti. Molecular Dynamics Simulations of Collagen-like Peptide Adsorption on Titanium-Based Material Surfaces , 2007 .
[65] Jeffrey J. Gray,et al. The interaction of proteins with solid surfaces. , 2004, Current opinion in structural biology.
[66] William J Welsh,et al. Prediction of the orientations of adsorbed protein using an empirical energy function with implicit solvation. , 2005, Langmuir : the ACS journal of surfaces and colloids.
[67] Candan Tamerler,et al. Molecular biomimetics: nanotechnology and bionanotechnology using genetically engineered peptides , 2009, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
[68] Ersin Emre Oren,et al. Probing the molecular mechanisms of quartz-binding peptides. , 2010, Langmuir : the ACS journal of surfaces and colloids.
[69] Gideon Schreiber,et al. Protein–surface interactions: challenging experiments and computations , 2009, Journal of molecular recognition : JMR.
[70] Robert A Latour,et al. Probing the conformation and orientation of adsorbed enzymes using side-chain modification. , 2009, Langmuir : the ACS journal of surfaces and colloids.
[71] Stefano Corni,et al. GolP: An atomistic force‐field to describe the interaction of proteins with Au(111) surfaces in water , 2009, J. Comput. Chem..
[72] Claudio Soto,et al. β-sheet breaker peptides inhibit fibrillogenesis in a rat brain model of amyloidosis: Implications for Alzheimer's therapy , 1998, Nature Medicine.
[73] Luigi Calzolai,et al. Protein--nanoparticle interaction: identification of the ubiquitin--gold nanoparticle interaction site. , 2010, Nano letters.
[74] T. R. Walsh,et al. Atomistic modelling of the interaction between peptides and carbon nanotubes , 2007 .
[75] Paul F. Barbara,et al. Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly , 2000, Nature.
[76] Gideon Schreiber,et al. A quantitative, real-time assessment of binding of peptides and proteins to gold surfaces. , 2011, Chemistry.
[77] K. Jain. The role of nanobiotechnology in drug discovery. , 2005, Drug discovery today.
[78] V. Helms,et al. Brownian dynamics simulations of simplified cytochrome c molecules in the presence of a charged surface. , 2004, The Journal of chemical physics.
[79] Sandor Vajda,et al. Protein-protein association kinetics and protein docking. , 2002, Current Opinion in Structural Biology.
[80] D. Quigley,et al. Computational techniques at the organic-inorganic interface in biomineralization. , 2008, Chemical reviews.
[81] Susanna Monti,et al. RAD16II β-Sheet Filaments onto Titanium Dioxide: Dynamics and Adsorption Properties , 2007 .
[82] P. Krebsbach,et al. Protein-to-Protein Interactions: Criteria Defining the Assembly of the Enamel Organic Matrix , 1998, Journal of dental research.
[83] M. Prato,et al. Functionalized carbon nanotubes in drug design and discovery. , 2008, Accounts of chemical research.
[84] Kurt Kremer,et al. Multiscale modeling of polymers on a surface: From ab initio density functional calculations of molecular adsorption to large-scale properties , 2005 .
[85] Burke,et al. Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.
[86] K. Schulten,et al. Molecular biomimetics: nanotechnology through biology , 2003, Nature materials.
[87] Luigi Delle Site,et al. Adsorption of alanine on a Ni(111) surface: A multiscale modeling oriented density functional study , 2006 .
[88] R. L. Rowley,et al. Simulating an electrochemical interface using charge dynamics , 2005 .
[89] B. Parviz,et al. Materials specificity and directed assembly of a gold-binding peptide. , 2006, Small.
[90] Vincenzo Carravetta,et al. Peptide-TiO2 surface interaction in solution by ab initio and molecular dynamics simulations. , 2006, The journal of physical chemistry. B.
[91] H. Matsui,et al. Applications of peptide and protein-based materials in bionanotechnology. , 2010, Chemical Society reviews.