A super-Gaussian Poisson–Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states
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Abrashkin A, Andelman D, Orland H (2007) Dipoloar Poisson–Boltzmann equation: ions and dipoles close to charge interface. Phys Rev Lett 99:077801
Alexov EG, Gunner MR (1997) Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. Biophys J 72:2075–2093
Alexov EG, Gunner MR (1999) Calculated protein and proton motions coupled to electron transfer: electron transfer from QA- to QB in bacterial photosynthetic reaction centers. Biochemistry 38:8253–8270
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci 98:10037–10041
Bates P, Wei GW, Zhao S (2008) Minimal molecular surfaces and their applications. J Comput Chem 29:380–391
Bates PW, Chen Z, Sun YH, Wei GW, Zhao S (2009) Geometric and potential driving formation and evolution of biomolecular surfaces. J Math Biol 59:193–231
Bohinc K, Bossa GV, May S (2017) Incorporation of ion and solvent structure into mean-field modeling of the electric double layer. Adv Colloid Interface Sci 249:220–233
Chakravorty A, Jia Z, Li L, Zhao S, Alexov E (2018a) Reproducing the ensemble average polar solvation energy of a protein from a single structure: Gaussian-based smooth dielectric function for macromolecular modeling. J Chem Theory Comput 14:1020–1032
Chakravorty A, Jia Z, Peng Y, Tajielyato N, Wang L, Alexov E (2018b) Gaussian-based smooth dielectric function: a surface-free approach for modeling macromolecular binding in solvents. Front Mol Biosci 5:25
Che J, Dzubiella J, Li B, McCammon JA (2008) Electrostatic free energy and its variations in implicit solvent models. J Phys Chem B 112:3058–3069
Chen M, Lu B (2011) TMSmesh: a robust method for molecular surface mesh generation using a trace technique. J Chem Theory Comput 7:203–212
Chen DA, Chen Z, Chen CJ, Geng WH, Wei GW (2011) Software news and update MIBPB: a software package for electrostatic analysis. J Comput Chem 32:756–770
Cheng L-T, Dzubiella J, McCammon JA, Li B (2007) Application of the level-set method to the solvation of nonpolar molecules. J Chem Phys 127:084503
Dai S, Li B, Liu J (2018) Convergence of phase-field free energy and boundary force for molecular solvation. Arch Ration Mech Anal 227:105–147
Deng W, Xu J, Zhao S (2018) On developing stable finite element methods for pseudo-time simulation of biomolecular electrostatics. J Comput Appl Math 330:456–474
Geng WH, Zhao S (2013) Fully implicit ADI schemes for solving the nonlinear Poisson–Boltzmann equation. Mol Math Biophys 1:109–123
Geng W, Zhao S (2017) A two-component matched interface and boundary (MIB) regularization for charge singularity in implicit solvation. J Comput Phys 351:25–39
Giard J, Macq B (2010) Molecular surface mesh generation by filtering electron density map. Int J Biomed Imaging 2010:923780
Grant JA, Pickup BT, Nicholls A (2001) A smooth permittivity function for Poisson–Boltzmann solvation methods. J Comput Chem 22:608–640
Hage KE, Hedin F, Gupta PK, Meuwly M, Karplus M (2018) Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size. eLife 7:e35560
Hammel M (2012) Validation of macromolecular flexibility in solution by small-angle X-ray scattering (SAXS). Eur Biophys J 41:789–799
Huggins DJ (2015) Quantifying the entropy of binding for water molecules in protein cavities by computing correlations. Biophys J 108:928–936
Im W, Beglov D, Roux B (1998) Continuum solvation model: computation of electrostatic forces from numerical solutions to the Poisson–Boltzmann equation. Comput Phys Commun 111:59–75
Jia Z, Li L, Chakravorty A, Alexov E (2017) Treating ion distribution with Gaussian-based smooth dielectric function in DelPhi. J Comput Chem 38:1974–1979
Koehl P, Orland H, Delarue M (2009) Beyond the Poisson–Boltzmann model: modeling biomolecular-water and water-water interactions. Phys Rev Lett 102:087801
Kokkinidis M, Glykos NM, Fadouloqlou VE (2012) Protein flexibility and enzymatic catalysis. Adv Protein Chem Struct Biol 87:181–218
Lee B, Richards FM (1973) Interpretation of protein structure: estimation of static accessibility. J Mol Biol 55:379–400
Li C, Li L, Zhang J, Alexov E (2012) Highly efficient and exact method for parallelization of gridbased algorithms and its implementation in DelPhi. J Comput Chem 33:1960–1966
Li C, Li L, Petukh M, Alexov E (2013a) Progress in developing Poisson–Boltzmann equation solvers. Mol Based Math Biol 1:42–62
Li L, Li C, Zhang Z, Alexov E (2013b) On the dielectric “constant” of proteins: smooth dielectric function for macromolecular modeling and its implementation in DelPhi. J Chem Theory Comput 9:2126–2136
Li L, Li C, Alexov E (2014) On the modeling of polar component of solvation energy using smooth Gaussian-based dielectric function. J Theory Comput Chem 13:1440002
Li L, Wang L, Alexov E (2015) On the energy components governing molecular recognition in the framework of continuum approaches. Front Mol Biosci 2:5
Lu BZ, Zhou YC, Holst MJ, McCammon JA (2008) Recent progress in numerical methods for the Poisson–Boltzmann equation in biophysical applications. Commun Comput Phys 3:973–1009
Mengistu DH, Bohing K, May S (2009) Poisson–Boltzmann model in a solvent of interacting Langevin dipoles. EPL (Europhys Lett) 88:14003
Ng J, Vora T, Krishnamurthy V, Chung S-H (2008) Estimating the dielectric constant of the channel protein and pore. Eur Biophys J 37:213–222
Nymeyer H, Zhou HX (2008) A method to determine dielectric constants in nonhomogeneous systems, application to biological membranes. Biophys J 94:1185–1193
Pang X, Zhou HX (2013) Poisson–Boltzmann calculations: van der Waals or molecular surface? Commun Comput Phys 13:1–12
Qiao ZH, Li ZL, Tang T (2006) A finite difference scheme for solving the nonlinear Poisson–Boltzmann equation modeling charged spheres. J Comput Math 24:252–264
Quillin ML, Wingfield PT, Matthews BW (2006) Determination of solvent content in cavities in IL-1$$\beta $$ using experimentally phased electron density. Proc Natl Acad Sci 103:19749–19753
Sanner M, Olson A, Spehner J (1996) Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38:305–320
Simonson T, Perahia D (1995) Internal interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution. Proc Natl Acad Sci 92:1082–1086
Song X (2002) An inhomogeneous model of protein dielectric properties: intrinsic polarizabilities of amino acids. J Chem Phys 116:9359
Takano K, Yamagata Y, Yutani K (2003) Buried water molecules contribute to the conformational stability of a protein. Protein Eng 16:5–9
Tian W, Zhao S (2014) A fast ADI algorithm for geometric flow equations in biomolecular surface generation. Int J Numer Method Biomed Eng 30:490–516
Voges D, Karshikoff A (1998) A model of a local dielectric constant in proteins. J Chem Phys 108:2219
Wang L, Li L, Alexov E (2015a) pKa predictions for proteins RNAs and DNAs with the Gaussian dielectric function using DelPhiPKa. Proteins Struct Funct Bioinform 83:2186–2197
Wang L, Zhang M, Alexov E (2015b) DelPhiPKa Web Server: predicting pKa of proteins RNAs and DNAs. Bioinformatics 32:614–615
Warshel A, Russell ST (1984) Calculations of electrostatic interactions in biological systems and in solutions. Q Rev Biophys 17:283–422
Warshel A, Sharma PK, Kato M, Parson WW (2006) Modeling electrostatic effects in proteins. Biochim Biophys Acta 1764:1647–1676
Wilson L, Zhao S (2016) Unconditionally stable time splitting methods for the electrostatic analysis of solvated biomolecules. Int J Numer Anal Modell 13:852–878
Yu Z, Holst MJ, Cheng Y, McCammon JA (2008) Feature-preserving adaptive mesh generation for molecular shape modeling and simulation. J Mol Graph Modell 26:1370–1380
Zhang Y, Xu G, Bajaj C (2006) Quality meshing of implicit solvation models of biomolecular structures. Comput Aided Geom Des 23:510–530
Zhao S (2011) Pseudo-time-coupled nonlinear models for biomolecular surface representation and solvation analysis. Int J Numer Method Biomed Eng 27:1964–1981
Zhao S (2014) Operator splitting ADI schemes for pseudo-time coupled nonlinear solvation simulations. J Comput Phys 257:1000–1021
Zhao Y, Kwan YY, Che J, Li B, McCammon JA (2013) Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation. J Chem Phys 139:024111