On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function.
暂无分享,去创建一个
[1] Lin Li,et al. On the Dielectric “Constant” of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi , 2013, Journal of chemical theory and computation.
[2] Ray Luo,et al. Numerical Poisson-Boltzmann Model for Continuum Membrane Systems. , 2013, Chemical physics letters.
[3] Anthony Nicholls,et al. Application of the Gaussian dielectric boundary in Zap to the prediction of protein pKa values , 2011, Proteins.
[4] Chandrajit L. Bajaj,et al. Quality meshing of implicit solvation models of biomolecular structures , 2006, Comput. Aided Geom. Des..
[5] J. Ponder,et al. Force fields for protein simulations. , 2003, Advances in protein chemistry.
[6] Nathan A. Baker,et al. Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[7] Emil Alexov,et al. Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants. , 2013, Communications in computational physics.
[8] W. Im,et al. Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation , 1998 .
[9] R. Nussinov,et al. The role of dynamic conformational ensembles in biomolecular recognition. , 2009, Nature chemical biology.
[10] Emil Alexov,et al. Progress in developing Poisson-Boltzmann equation solvers , 2013, Molecular Based Mathematical Biology.
[11] Robert C. Harris,et al. Influence of Grid Spacing in Poisson-Boltzmann Equation Binding Energy Estimation. , 2013, Journal of chemical theory and computation.
[12] Emil Alexov,et al. Rapid grid‐based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects , 2002, J. Comput. Chem..
[13] Carl Caleman,et al. Proteins, lipids, and water in the gas phase. , 2011, Macromolecular bioscience.
[14] James F. Blinn,et al. A generalization of algebraic surface drawing , 1982, SIGGRAPH.
[15] R. Luo,et al. Reducing grid-dependence in finite-difference Poisson-Boltzmann calculations. , 2012, Journal of chemical theory and computation.
[16] E. Alexov,et al. Calculated protein and proton motions coupled to electron transfer: electron transfer from QA- to QB in bacterial photosynthetic reaction centers. , 1999, Biochemistry.
[17] Gerhard Hummer,et al. Water clusters in nonpolar cavities. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[18] Martin F. Jarrold,et al. CONFORMATIONS, UNFOLDING, AND REFOLDING OF APOMYOGLOBIN IN VACUUM : AN ACTIVATION BARRIER FOR GAS-PHASE PROTEIN FOLDING , 1997 .
[19] Robert C. Harris,et al. A Stochastic Solver of the Generalized Born Model , 2013 .
[20] M. Gilson,et al. Prediction of pH-dependent properties of proteins. , 1994, Journal of molecular biology.
[21] M. L. Connolly. Analytical molecular surface calculation , 1983 .
[22] Nathan A. Baker,et al. Biomolecular electrostatics and solvation: a computational perspective , 2012, Quarterly Reviews of Biophysics.
[23] Nathan A. Baker,et al. Differential geometry based solvation model I: Eulerian formulation , 2010, J. Comput. Phys..
[24] B. Honig,et al. A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation , 1991 .
[25] B. García-Moreno E.,et al. High tolerance for ionizable residues in the hydrophobic interior of proteins , 2008, Proceedings of the National Academy of Sciences.
[26] Gerhard Hummer,et al. Water in the polar and nonpolar cavities of the protein interleukin-1β. , 2010, The journal of physical chemistry. B.
[27] J. Andrew Grant,et al. A smooth permittivity function for Poisson–Boltzmann solvation methods , 2001, J. Comput. Chem..
[28] D. Case,et al. Generalized Born Models of Macromolecular Solvation Effects , 2001 .
[29] M. Gunner,et al. MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease , 2011, Proteins.
[30] J Andrew McCammon,et al. Electrostatic Free Energy and Its Variations in Implicit Solvent Models , 2022 .
[31] Chuan Li,et al. Highly efficient and exact method for parallelization of grid‐based algorithms and its implementation in DelPhi , 2012, J. Comput. Chem..
[32] A. Warshel,et al. Electrostatic effects in macromolecules: fundamental concepts and practical modeling. , 1998, Current opinion in structural biology.
[33] N. Oldham,et al. Evidence for the Preservation of Native Inter- and Intra-Molecular Hydrogen Bonds in the Desolvated FK-Binding Protein·FK506 Complex Produced by Electrospray Ionization , 2012, Journal of The American Society for Mass Spectrometry.
[34] Jim Warwicker,et al. pKa predictions with a coupled finite difference Poisson–Boltzmann and Debye–Hückel method , 2011, Proteins.
[35] Jose M. Sanchez-Ruiz,et al. Modulation of buried ionizable groups in proteins with engineered surface charge. , 2010, Journal of the American Chemical Society.
[36] A. Broom,et al. Kinetic stability of the streptavidin-biotin interaction enhanced in the gas phase. , 2012, Journal of the American Chemical Society.
[37] Lin Li,et al. DelPhi: a comprehensive suite for DelPhi software and associated resources , 2012, BMC biophysics.
[38] Zhe Zhang,et al. On the role of electrostatics in protein–protein interactions , 2011, Physical biology.
[39] Barry Honig,et al. Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions† , 2001 .
[40] Barry Honig,et al. Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification , 1986, Proteins.
[41] Emil Alexov,et al. Role of the protein side‐chain fluctuations on the strength of pair‐wise electrostatic interactions: Comparing experimental with computed pKas , 2002, Proteins.
[42] B. Lee,et al. The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.
[43] Huan-Xiang Zhou,et al. Poisson-Boltzmann Calculations: van der Waals or Molecular Surface? , 2013, Communications in computational physics.
[44] Shan Zhao,et al. Variational approach for nonpolar solvation analysis. , 2012, The Journal of chemical physics.
[45] Emil Alexov,et al. Protonation and pK changes in protein–ligand binding , 2013, Quarterly Reviews of Biophysics.
[46] Sarah L. Williams,et al. Progress in the prediction of pKa values in proteins , 2011, Proteins.
[47] Lisa Yan,et al. A fast and accurate computational approach to protein ionization , 2008, Protein science : a publication of the Protein Society.
[48] J. A. Grant,et al. A Gaussian Description of Molecular Shape , 1995 .