PL EN


Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
2015 | 3 | 1 |
Tytuł artykułu

SDPBS Web Server for Calculation of Electrostatics of Ionic Solvated Biomolecules

Treść / Zawartość
Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. We recently developed a PBE solver library, called SDPBS, that incorporates the finite element, finite difference, solution decomposition, domain decomposition, and multigrid methods. To make SDPBS more accessible to the scientific community, we present an SDPBS web server in this paper that allows clients to visualize and manipulate the molecular structure of a biomolecule, and to calculate PBE solutions in a remote and user friendly fashion. The web server is available on the website https://lsextrnprod.uwm.edu/electrostatics/.
Wydawca
Rocznik
Tom
3
Numer
1
Opis fizyczny
Daty
otrzymano
2015-09-17
zaakceptowano
2015-11-19
online
2015-11-30
Twórcy
autor
  • Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee,
    WI 53201-0413, USA
autor
  • Department of Computer Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53201-0413, USA
autor
  • Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee,
    WI 53201-0413, USA
autor
  • Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee,
    WI 53201-0413, USA
autor
  • Department of Computer Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53201-0413, USA
Bibliografia
  • [1] J. Ahrens, B. Geveci, and C. Law. ParaView: An end user tool for large data visualization. In C. Hansen and C. Johnson,editors, The Visualization Handbook, pages 717–731. Academic Press, 2005.
  • [2] N. Baker, M. Holst, and F. Wang. Adaptive multilevel finite element solution of the Poisson–Boltzmann equation II. Refinementat solvent-accessible surfaces in biomolecular systems. Journal of Computational Chemistry, 21(15):1343–1352, 2000.[Crossref]
  • [3] N. A. Baker, D. Sept, S. Joseph, M. Holst, and J. A. McCammon. Electrostatics of nanosystems: Application to microtubulesand the ribosome. Proc. Natl. Acad. Sci. USA, 98(18):10037–10041, 2001.[Crossref]
  • [4] N.A. Baker, D. Sept, M.J. Holst, and J.A.McCammon. The adaptivemultilevel finite element solution of the Poisson-Boltzmannequation on massively parallel computers. IBM Journal of Research and Development, 45(3.4):427–438, 2001.[Crossref]
  • [5] S. Balay, J. Brown, K. Buschelman, V. Eijkhout,W.D. Gropp, D. Kaushik, M.G. Knepley, L.C. McInnes, B.F. Smith, and H. Zhang.PETSc users manual. Technical Report ANL-95/11 - Revision 3.1, Argonne National Laboratory, 2010.
  • [6] S. Balay, J. Brown, K. Buschelman, W.D. Gropp, D. Kaushik, M.G. Knepley, L.C. McInnes, B.F. Smith, and H. Zhang. PETScWeb page, 2012. http://www.mcs.anl.gov/petsc.
  • [7] Donald Bashford and Martin Karplus. pKa’s of ionizable groups in proteins: atomic detail from a continuum electrostaticmodel. Biochemistry, 29(44):10219–10225, 1990.[Crossref]
  • [8] C. Bertonati, B. Honig, and E. Alexov. Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein bindingfree energies. Biophysical Journal, 92(6):1891–1899, 2007.[Crossref]
  • [9] Kenneth J Breslauer, David P Remeta, Wan-Yin Chou, Robert Ferrante, James Curry, Denise Zaunczkowski, James G Snyder,and Luis A Marky. Enthalpy-entropy compensations in drug-DNA binding studies. Proceedings of the National Academy ofSciences, 84(24):8922–8926, 1987.
  • [10] D. Chen, Z. Chen, C. Chen, W. Geng, and G. Wei. MIBPB: A software package for electrostatic analysis. Journal of ComputationalChemistry, 32(4):756–770, 2011.[Crossref]
  • [11] L. Chen, M. J. Holst, and J. Xu. The finite element approximation of the nonlinear Poisson-Boltzmann equation. SIAM Journalon Numerical Analysis, 45(6):2298–2320, 2007.[Crossref]
  • [12] I.L. Chern, J.G. Liu, and W.C. Wang. Accurate evaluation of electrostatics for macromolecules in solution. Methods andApplications of Analysis, 10(2):309–328, 2003.
  • [13] M. E. Davis, J. D. Madura, B. A. Luty, and J. A. McCammon. Electrostatics and diffusion of molecules in solution: Simulationswith the University of Houston Browian dynamics program. Comp. Phys. Comm., 62:187–197, 1991.[Crossref]
  • [14] M. E. Davis and J. A. McCammon. Solving the finite difference linearized Poisson-Boltzmann equation: A comparison ofrelaxation and conjugate gradient methods. J. Comp. Chem., 10:386–391, 1989.
  • [15] J. E. Dennis, Jr. and R. B. Schnabel. Numerical Methods for Unconstrained Optimization and Nonlinear Equations, volume 16of Classics in Applied Mathematics. SIAM, Philadelphia, PA, 1996.
  • [16] T.J. Dolinsky, J.E. Nielsen, J.A. McCammon, and N.A. Baker. PDB2PQR: An automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations. Nucleic Acids Research, 32(suppl 2):W665, 2004.[Crossref]
  • [17] David Eisenberg and Andrew D McLachlan. Solvation energy in protein folding and binding. Nature, 319:199 – 203, 1986.
  • [18] Marcia O Fenley, Robert C Harris, B Jayaram, and Alexander H Boschitsch. Revisiting the association of cationic groovebindingdrugs to DNA using a Poisson-Boltzmann approach. Biophysical Journal, 99(3):879–886, 2010.[Crossref]
  • [19] F. Fogolari, A. Brigo, and H. Molinari. The Poisson-Boltzmann equation for biomolecular electrostatics: A tool for structuralbiology. J. Mol. Recognit., 15(6):377–392, 2002.[Crossref]
  • [20] C. García-García and D.E. Draper. Electrostatic interactions in a peptide-RNA complex. J. Mol. Biol., 331(1):75–88, 2003.
  • [21] Weihua Geng and Robert Krasny. A treecode-accelerated boundary integral Poisson-Boltzmann solver for electrostatics ofsolvated biomolecules. J. Comput. Phys., 247:62–78, 2013.
  • [22] Weihua Geng, Sining Yu, and Guowei Wei. Treatment of charge singularities in implicit solvent models. The Journal ofChemical Physics, 127(11):114106, 2007.[Crossref]
  • [23] M.K. Gilson, A. Rashin, R. Fine, and B. Honig. On the calculation of electrostatic interactions in proteins. Journal ofMolecularBiology, 184(3):503–516, 1985.[Crossref]
  • [24] M. Holst, N. Baker, and F.Wang. Adaptive multilevel finite element solution of the Poisson-Boltzmann equation I: Algorithmsand examples. J. Comput. Chem., 21:1319–1342, 2000.[Crossref]
  • [25] M. Holst, J. A. McCammon, Z. Yu, Y. Zhou, and Y. Zhu. Adaptive finite element modeling techniques for the Poisson-Boltzmannequation. Communications in Computational Physics, 11(1):179–214, 2012.
  • [26] B. Honig and A. Nicholls. Classical electrostatics in biology and chemistry. Science, 268:1144–1149, May 1995.
  • [27] W. Humphrey, A. Dalke, and K. Schulten. VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1):33–38,1996.[Crossref]
  • [28] R.M. Jackson and M.J.E. Sternberg. A continuummodel for protein-protein interactions: Application to the docking problem.Journal of Molecular Biology, 250(2):258–275, 1995.[Crossref]
  • [29] Y. Jiang, J. Ying, and D. Xie. A Poisson-Boltzmann equation test model for protein in spherical solute region and its applications.Molecular Based Mathematical Biology, 2:86–97, 2014. Open Access.
  • [30] Sunhwan Jo, Miklos Vargyas, Judit Vasko-Szedlar, Benoît Roux, and Wonpil Im. PBEQ-solver for online visualization of electrostaticpotential of biomolecules. Nucleic Acids Research, 36(suppl 2):W270–W275, 2008.[Crossref]
  • [31] John G Kirkwood and Jacques C Poirier. The statistical mechanical basis of the Debye–hüekel theory of strong electrolytes.The Journal of Physical Chemistry, 58(8):591–596, 1954.[Crossref]
  • [32] Isaac Klapper, Ray Hagstrom, Richard Fine, Kim Sharp, and Barry Honig. Focusing of electric fields in the active site of cu-znsuperoxide dismutase: Effects of ionic strength and amino-acid modification. Proteins: Structure, Function, and Bioinformatics,1(1):47–59, 1986.
  • [33] Lev Davidovich Landau and EM Lifshitz. Statistical physics, part I. Course of Theoretical Physics, 5:468, 1980.
  • [34] J. Li and D. Xie. An effective minimization protocol for solving a size-modified Poisson-Boltzmann equation for biomoleculein ionic solvent. International Journal of Numerical Analysis and Modeling, 12(2):286–301, 2015.
  • [35] J. Li and D. Xie. A new linear Poisson-Boltzmann equation and finite element solver by solution decomposition approach.Communications in Mathematical Sciences, 13(2):315–325, 2015. International Press.[Crossref]
  • [36] Tiantian Liu, Minxin Chen, and Benzhuo Lu. Parameterization for molecular gaussian surface and a comparison study ofsurface mesh generation. Journal of molecular modeling, 21(5):1–14, 2015.
  • [37] A. Logg, K.-A. Mardal, and G. N. Wells, editors. Automated Solution of Differential Equations by the Finite Element Method,volume 84 of Lecture Notes in Computational Science and Engineering. Springer Verlag, 2012.
  • [38] B. Lu, Y. Zhou, M.J. Holst, and J.A. McCammon. Recent progress in numerical methods for the Poisson-Boltzmann equationin biophysical applications. Commun. Comput. Phys., 3(5):973–1009, 2008.
  • [39] Benzhuo Lu, Xiaolin Cheng, and J Andrew McCammon. “New-version-fast-multipole-method” accelerated electrostatic calculationsin biomolecular systems. Journal of Computational Physics, 226(2):1348–1366, 2007.[Crossref]
  • [40] Ray Luo, Laurent David, and Michael K Gilson. Accelerated Poisson–Boltzmann calculations for static and dynamic systems.Journal of Computational Chemistry, 23(13):1244–1253, 2002.[Crossref]
  • [41] Gerald S Manning. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties ofpolynucleotides. Quarterly Reviews of Biophysics, 11(02):179–246, 1978.[Crossref]
  • [42] Vinod K Misra, Kim A Sharp, Richard A Friedman, and Barry Honig. Salt effects on ligand-DNA binding: Minor groove bindingantibiotics. Journal of Molecular Biology, 238(2):245–263, 1994.
  • [43] Jens Erik Nielsen and J Andrew McCammon. Calculating pKa values in enzymeactive sites. Protein Science, 12(9):1894–1901,2003.[Crossref]
  • [44] J. Nocedal and S. Wright. Numerical Optimization. Springer Series in Operations Research and Financial Engineering.Springer, New York, second edition, 2006.
  • [45] Michael J Potter, Michael K Gilson, and J Andrew McCammon. Small molecule pKa prediction with continuum electrostaticscalculations. Journal of the American Chemical Society, 116(22):10298–10299, 1994.[Crossref]
  • [46] Pengyu Ren, Jaehun Chun, Dennis G Thomas, Michael J Schnieders, Marcelo Marucho, Jiajing Zhang, and Nathan A Baker.Biomolecular electrostatics and solvation: A computational perspective. Quarterly Reviews of Biophysics, 45(04):427–491,2012.[Crossref]
  • [47] W. Rocchia, E. Alexov, and B. Honig. Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multipledielectric constants and multivalent ions. J. Phys. Chem. B, 105:6507–6514, 2001.[Crossref]
  • [48] B. Roux and T. Simonson. Implicit solvent models. Biophys. Chem., 78:1–20, 1999.[Crossref]
  • [49] W. Rudin. Functional Analysis. McGraw-Hill, New York, 2nd edition, 1991.
  • [50] Subhra Sarkar, ShawnWitham, Jie Zhang,Maxim Zhenirovskyy,Walter Rocchia, and Emil Alexov. Delphi web server: A comprehensiveonline suite for electrostatic calculations of biological macromolecules and their complexes. Communicationsin Computational Physics, 13(1):269, 2013.
  • [51] Schrödinger, LLC. The PyMOL molecular graphics system, version 1.3r1. August 2010.
  • [52] D. Sitkoff, K. A Sharp, and B. Honig. Accurate calculation of hydration free energies using macroscopic solvent models. J.Phys. Chem., 98(7):1978–1988, 1994.
  • [53] N. Smith, S. Witham, S. Sarkar, J. Zhang, L. Li, C. Li, and E. Alexov. DelPhi web server v2: Incorporating atomic-style geometricalfigures into the computational protocol. Bioinformatics, 28(12):1655–1657, 2012.[Crossref]
  • [54] C. Tanford. Physical Chemistry of Macromolecules. John Wiley & Sons, New York, NY, 1961.
  • [55] Samir Unni, Yong Huang, Robert M Hanson, Malcolm Tobias, Sriram Krishnan, Wilfred W Li, Jens E Nielsen, and Nathan ABaker. Web servers and services for electrostatics calculations with APBS and PDB2PQR. J. Comput. Chem., 32(7):1488–1491, 2011.[Crossref]
  • [56] J.A. Wagoner and N.A. Baker. Assessing implicit models for nonpolar mean solvation forces: the importance of dispersionand volume terms. Proceedings of the National Academy of Sciences, 103(22):8331, 2006.
  • [57] ChanghaoWang, JunWang, Qin Cai, Zhilin Li, Hong-Kai Zhao, and Ray Luo. Exploring accurate Poisson–Boltzmann methodsfor biomolecular simulations. Computational and Theoretical Chemistry, 1024:34–44, 2013.
  • [58] Philip Weetman, Saul Goldman, and CG Gray. Use of the Poisson-Boltzmann equation to estimate the electrostatic freeenergy barrier for dielectric models of biological ion channels. The Journal of Physical Chemistry B, 101(31):6073–6078,1997.[Crossref]
  • [59] D. Xie. New solution decomposition and minimization schemes for Poisson-Boltzmann equation in calculation of biomolecularelectrostatics. J. Comput. Phys., 275:294–309, 2014.
  • [60] D. Xie, Y. Jiang, P. Brune, and L.R. Scott. A fast solver for a nonlocal dielectric continuum model. SIAM J. Sci. Comput.,34(2):B107–B126, 2012.
  • [61] D. Xie, Y. Jiang, and L.R. Scott. Eflcient algorithms for a nonlocal dielectric model for protein in ionic solvent. SIAM J. Sci.Comput., 38:B1267–1284, 2013.
  • [62] D. Xie and S. Zhou. A new minimization protocol for solving nonlinear Poisson-Boltzmann mortar finite element equation.BIT Num. Math., 47:853–871, 2007.
  • [63] Dexuan Xie and Jiao Li. A new analysis of electrostatic free energy minimization and Poisson-Boltzmann equation for proteinin ionic solvent. Nonlinear Analysis: Real World Applications, 21:185–196, 2015.[Crossref]
  • [64] Dong Xu and Yang Zhang. Generating triangulated macromolecular surfaces by Euclidean distance transform. PloS ONE,4(12):e8140, 2009.
  • [65] J. Ying and D. Xie. A new finite element and finite difference hybrid method for computing electrostatics of ionic solvatedbiomolecule. Journal of Computational Physics, 298:636–651, 2015.
  • [66] Z. Yu, M.J. Holst, Y. Cheng, and J.A. McCammon. Feature-preserving adaptive mesh generation for molecular shape modelingand simulation. Journal of Molecular Graphics and Modelling, 26(8):1370–1380, 2008.
  • [67] Y. C. Zhou, M. Holst, and J. A. McCammon. A nonlinear elasticity model of macromolecular conformational change inducedby electrostatic forces. Journal of Mathematical Analysis and Applications, 340(1):135–164, 2008.
  • [68] Z. Zhou, P. Payne, M. Vasquez, N. Kuhn, and M. Levitt. Finite-difference solution of the Poisson-Boltzmann equation: Completeelimination of self-energy. Journal of Computational Chemistry, 17(11):1344–1351, 1996. [Crossref]
Typ dokumentu
Bibliografia
Identyfikatory
Identyfikator YADDA
bwmeta1.element.doi-10_1515_mlbmb-2015-0011
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.