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Molecular Simulation Volume 8, 1992 - Issue 6
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Original Articles

Molecular Dynamics Simulations in Heterogeneous Dielectrica and Debye-Hückel Media - Application to the Protein Bovine Pancreatic Trypsin Inhibitor

C. Niedermeier Department of Physics, Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Avenue, Urbana, IL, 61801, U.S.A.; Gesellschaft für Strahlen- und Umweltforschung, Ingolstädter Landstraße 1, D-8042, Neuherberg, FRG
&
K. Schulten Department of Physics, Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Avenue, Urbana, IL, 61801, U.S.A.
Pages 361-387 | Received 01 Aug 1980, Accepted 01 Sep 1990, Published online: 23 Sep 2006

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D.A. Mac Dónaill & D.A. Morton-blake. (1996) Polarization effects on amino-acid and peptide conformations. Philosophical Magazine B 73:1, pages 139-146.
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PieterF. W. Stouten, Cornelius Frömmel, Haruki Nakamura & Chris Sander. (1993) An Effective Solvation Term Based on Atomic Occupancies for Use in Protein Simulations. Molecular Simulation 10:2-6, pages 97-120.
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Walter Alvarado, Joshua Moller, Andrew L. Ferguson & Juan J. de Pablo. (2021) Tetranucleosome Interactions Drive Chromatin Folding. ACS Central Science 7:6, pages 1019-1027.
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Johannes Kraus, Svetoslav Nakov & Sergey Repin. (2020) Reliable Computer Simulation Methods for Electrostatic Biomolecular Models Based on the Poisson–Boltzmann Equation. Computational Methods in Applied Mathematics 20:4, pages 643-676.
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Li Xiao, Changhao Wang, Xiang Ye & Ray Luo. (2016) Charge Central Interpretation of the Full Nonlinear PB Equation: Implications for Accurate and Scalable Modeling of Solvation Interactions. The Journal of Physical Chemistry B 120:33, pages 8707-8721.
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Federico Fogolari, Alessandra Corazza & Gennaro Esposito. (2015) Accuracy assessment of the linear Poisson-Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid-protein complexes. Journal of Computational Chemistry 36:9, pages 585-596.
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L. G. Stanton & M. S. Murillo. (2015) Unified description of linear screening in dense plasmas. Physical Review E 91:3.
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Li Xiao, Changhao Wang & Ray Luo. (2014) Recent progress in adapting Poisson–Boltzmann methods to molecular simulations. Journal of Theoretical and Computational Chemistry 13:03, pages 1430001.
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Changhao Wang, Jun Wang, Qin Cai, Zhilin Li, Hong-Kai Zhao & Ray Luo. (2013) Exploring accurate Poisson–Boltzmann methods for biomolecular simulations. Computational and Theoretical Chemistry 1024, pages 34-44.
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Li Xiao, Qin Cai, Xiang Ye, Jun Wang & Ray Luo. (2013) Electrostatic forces in the Poisson-Boltzmann systems. The Journal of Chemical Physics 139:9.
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Ninad V. Prabhu, Manoranjan Panda, Qingyi Yang & Kim A. Sharp. (2008) Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules. Journal of Computational Chemistry 29:7, pages 1113-1130.
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Michael J. Schnieders, Nathan A. Baker, Pengyu Ren & Jay W. Ponder. (2007) Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. The Journal of Chemical Physics 126:12.
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Ninad V. Prabhu, Peijuan Zhu & Kim A. Sharp. (2004) Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method. Journal of Computational Chemistry 25:16, pages 2049-2064.
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Michael Feig, Alexey Onufriev, Michael S. Lee, Wonpil Im, David A. Case & Charles L. BrooksIIIIII. (2003) Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. Journal of Computational Chemistry 25:2, pages 265-284.
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Bernhard Egwolf & Paul Tavan. (2004) Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution. The Journal of Chemical Physics 120:4, pages 2056-2068.
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Qiang Lu & Ray Luo. (2003) A Poisson–Boltzmann dynamics method with nonperiodic boundary condition. The Journal of Chemical Physics 119:21, pages 11035-11047.
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Federico Fogolari, Alessandro Brigo & Henriette Molinari. (2003) Protocol for MM/PBSA Molecular Dynamics Simulations of Proteins. Biophysical Journal 85:1, pages 159-166.
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Bernhard Egwolf & Paul Tavan. (2003) Continuum description of solvent dielectrics in molecular-dynamics simulations of proteins. The Journal of Chemical Physics 118:5, pages 2039-2056.
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F. Fogolari, A. Brigo & H. Molinari. (2002) The Poisson–Boltzmann equation for biomolecular electrostatics: a tool for structural biology. Journal of Molecular Recognition 15:6, pages 377-392.
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Ray Luo, Laurent David & Michael K. Gilson. (2002) Accelerated Poisson-Boltzmann calculations for static and dynamic systems. Journal of Computational Chemistry 23:13, pages 1244-1253.
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Kim A. Sharp. 2002. Computational Approaches to Biochemical Reactivity. Computational Approaches to Biochemical Reactivity 199 235 .
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Michael J. Potter, Paul D. Kirchhoff, Heather A. Carlson & J. Andrew McCammon. (1999) Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model. Journal of Computational Chemistry 20:9, pages 956-970.
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Mafalda Nina, Wonpil Im & Benoı̂t Roux. (1999) Optimized atomic radii for protein continuum electrostatics solvation forces. Biophysical Chemistry 78:1-2, pages 89-96.
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Koichi Tazaki & Kentaro Shimizu. (1998) Molecular Dynamics Simulations in Aqueous Solution:  Application to Free Energy Calculation of Oligopeptides. The Journal of Physical Chemistry B 102:33, pages 6419-6424.
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Wonpil Im, Dmitrii Beglov & Benoît Roux. (1998) Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Computer Physics Communications 111:1-3, pages 59-75.
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António M. Baptista, Paulo J. Martel & Steffen B. Petersen. (1997) Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration. Proteins: Structure, Function, and Genetics 27:4, pages 523-544.
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