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Volumn , Issue , 2007, Pages 4563-4569

Efficient optimization of electrostatic interactions between biomolecules

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BIOMOLECULES; COMPUTATION THEORY; CONSTRAINED OPTIMIZATION; LIGANDS; PROBLEM SOLVING;

EID: 62749169136     PISSN: 07431546     EISSN: 25762370     Source Type: Conference Proceeding    
DOI: 10.1109/CDC.2007.4434808     Document Type: Conference Paper
Times cited : (1)

References (66)
  • 1
  • 3
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • B. Honig and A. Nicholls, "Classical electrostatics in biology and chemistry," Science, vol. 268, pp. 1144-1149, 1995.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 4
    • 33947468892 scopus 로고
    • Theory of protein titration curves I. General equations for impenetrable spheres
    • C. Tanford and J. G. Kirkwood, "Theory of protein titration curves I. General equations for impenetrable spheres," Journal of the American Chemical Society, vol. 59, pp. 5333-5339, 1957.
    • (1957) Journal of the American Chemical Society , vol.59 , pp. 5333-5339
    • Tanford, C.1    Kirkwood, J.G.2
  • 7
    • 0001031179 scopus 로고
    • Proteins: A theoretical perspective of dynamics, structure and thermodynamics
    • C. L. Brooks, III, M. Karplus, and B. M. Pettitt, "Proteins: A theoretical perspective of dynamics, structure and thermodynamics," Advances in Chemical Phyics., vol. 71, pp. 1-249, 1988.
    • (1988) Advances in Chemical Phyics , vol.71 , pp. 1-249
    • Brooks III, C.L.1    Karplus, M.2    Pettitt, B.M.3
  • 9
    • 0001458825 scopus 로고
    • The aqueous solvation of water: A comparison of continuum methods with molecular dynamics
    • S. W. Rick and B. J. Berne, "The aqueous solvation of water: A comparison of continuum methods with molecular dynamics," Journal of the American Chemical Society, vol. 116, pp. 3949-3954, 1994.
    • (1994) Journal of the American Chemical Society , vol.116 , pp. 3949-3954
    • Rick, S.W.1    Berne, B.J.2
  • 11
    • 0020475509 scopus 로고
    • Calculation of the electric potential in the active site cleft due to alpha-helix dipoles
    • J. Warwicker and H. C. Watson, "Calculation of the electric potential in the active site cleft due to alpha-helix dipoles," Journal of Molecular Biology, vol. 157, pp. 671-679, 1982.
    • (1982) Journal of Molecular Biology , vol.157 , pp. 671-679
    • Warwicker, J.1    Watson, H.C.2
  • 13
    • 18744372751 scopus 로고    scopus 로고
    • Calculation of absolute protein-ligand binding free energy from computer simulations
    • H.-J. Woo and B. Roux, "Calculation of absolute protein-ligand binding free energy from computer simulations," Proceedings of the National Academy of Sciences of the USA, vol. 102, no. 19, pp. 6825-6830, 2004.
    • (2004) Proceedings of the National Academy of Sciences of the USA , vol.102 , Issue.19 , pp. 6825-6830
    • Woo, H.-J.1    Roux, B.2
  • 14
    • 33751385054 scopus 로고
    • Macroscopic models of aqueous solutions: Biological and chemical applications
    • B. Honig, K. Sharp, and A. S. Yang, "Macroscopic models of aqueous solutions: Biological and chemical applications," Journal of Physical Chemistry, vol. 97, no. 6, pp. 1101-1109, 1993.
    • (1993) Journal of Physical Chemistry , vol.97 , Issue.6 , pp. 1101-1109
    • Honig, B.1    Sharp, K.2    Yang, A.S.3
  • 15
    • 0031165571 scopus 로고    scopus 로고
    • Optimization of electrostatic binding free energy
    • L.-P. Lee and B. Tidor, "Optimization of electrostatic binding free energy," Journal of Chemical Physics, vol. 106, pp. 8681-8690, 1997.
    • (1997) Journal of Chemical Physics , vol.106 , pp. 8681-8690
    • Lee, L.-P.1    Tidor, B.2
  • 16
    • 21944443282 scopus 로고    scopus 로고
    • Optimizing electrostatic affinity in ligand-receptor binding: Theory, computation, and ligand properties
    • E. Kangas and B. Tidor, "Optimizing electrostatic affinity in ligand-receptor binding: Theory, computation, and ligand properties," Journal of Chemical Physics, vol. 109, pp. 7522-7545, 1998.
    • (1998) Journal of Chemical Physics , vol.109 , pp. 7522-7545
    • Kangas, E.1    Tidor, B.2
  • 17
    • 0033134360 scopus 로고    scopus 로고
    • Charge optimization leads to favorable electrostatic binding free energy
    • _, "Charge optimization leads to favorable electrostatic binding free energy," Physical Review E, vol. 59, no. 5, pp. 5958-5961, 1999.
    • (1999) Physical Review E , vol.59 , Issue.5 , pp. 5958-5961
    • Kangas, E.1    Tidor, B.2
  • 18
    • 0001192934 scopus 로고    scopus 로고
    • Electrostatic specificity in molecular ligand design
    • _, "Electrostatic specificity in molecular ligand design," Journal of Chemical Physics, vol. 112, pp. 9120-9131, 2000.
    • (2000) Journal of Chemical Physics , vol.112 , pp. 9120-9131
    • Kangas, E.1    Tidor, B.2
  • 19
    • 0031891022 scopus 로고    scopus 로고
    • Computation of electrostatic complements to proteins: A case of charge stabilized binding
    • L. T. Chong, S. E. Dempster, Z. S. Hendsch, L.-P. Lee, and B. Tidor, "Computation of electrostatic complements to proteins: A case of charge stabilized binding," Protein Science, vol. 7, no. 1, pp. 206-210, 1998.
    • (1998) Protein Science , vol.7 , Issue.1 , pp. 206-210
    • Chong, L.T.1    Dempster, S.E.2    Hendsch, Z.S.3    Lee, L.-P.4    Tidor, B.5
  • 20
    • 0035107570 scopus 로고    scopus 로고
    • Optimization of binding electrostatics: Charge complementarity in the barnase-barstar protein complex
    • L.-P. Lee and B. Tidor, "Optimization of binding electrostatics: Charge complementarity in the barnase-barstar protein complex," Protein Science, vol. 10, pp. 362-377, 2001.
    • (2001) Protein Science , vol.10 , pp. 362-377
    • Lee, L.-P.1    Tidor, B.2
  • 21
    • 0035160537 scopus 로고    scopus 로고
    • Barstar is electrostatically optimized for tight-binding to barnase
    • _, "Barstar is electrostatically optimized for tight-binding to barnase," Nature Structural Biology, vol. 8, pp. 73-76, 2001.
    • (2001) Nature Structural Biology , vol.8 , pp. 73-76
    • Lee, L.-P.1    Tidor, B.2
  • 22
    • 0034824313 scopus 로고    scopus 로고
    • Electrostatic complementarity at ligand binding sites: Application to chorismate mutase
    • E. Kangas and B. Tidor, "Electrostatic complementarity at ligand binding sites: Application to chorismate mutase," Journal of Physical Chemistry, vol. 105, pp. 880-888, 2001.
    • (2001) Journal of Physical Chemistry , vol.105 , pp. 880-888
    • Kangas, E.1    Tidor, B.2
  • 23
    • 0034825821 scopus 로고    scopus 로고
    • Optimizing ligand charges for maximum binding affinity. A solvated interaction energy approach
    • T. Sulea and E. O. Purisima, "Optimizing ligand charges for maximum binding affinity. A solvated interaction energy approach," Journal of Physical Chemistry B, vol. 105, no. 4, pp. 889-899, 2001.
    • (2001) Journal of Physical Chemistry B , vol.105 , Issue.4 , pp. 889-899
    • Sulea, T.1    Purisima, E.O.2
  • 24
    • 0038298792 scopus 로고    scopus 로고
    • Profiling charge complementarity and selectivity for binding at the protein surface
    • _, "Profiling charge complementarity and selectivity for binding at the protein surface," Biophysical Journal, vol. 84, no. 5, pp. 2883-2896, 2003.
    • (2003) Biophysical Journal , vol.84 , Issue.5 , pp. 2883-2896
    • Sulea, T.1    Purisima, E.O.2
  • 25
    • 3142661052 scopus 로고    scopus 로고
    • Charge optimization of the interface between protein kinases and their ligands
    • P. A. Sims, C. F. Wong, and J. A. McCammon, "Charge optimization of the interface between protein kinases and their ligands," Journal of Computational Chemistry, vol. 25, no. 11, pp. 1416-1429, 2004.
    • (2004) Journal of Computational Chemistry , vol.25 , Issue.11 , pp. 1416-1429
    • Sims, P.A.1    Wong, C.F.2    McCammon, J.A.3
  • 26
    • 4344595498 scopus 로고    scopus 로고
    • Escherichia coli glutaminyl-tRNA synthetase is electrostatically optimized for binding of its cognate substrates
    • D. F. Green and B. Tidor, "Escherichia coli glutaminyl-tRNA synthetase is electrostatically optimized for binding of its cognate substrates," Journal of Molecular Biology, vol. 342, no. 2, pp. 435-452, 2004.
    • (2004) Journal of Molecular Biology , vol.342 , Issue.2 , pp. 435-452
    • Green, D.F.1    Tidor, B.2
  • 27
    • 24644518008 scopus 로고    scopus 로고
    • Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface
    • _, "Design of improved protein inhibitors of HIV-1 cell entry: Optimization of electrostatic interactions at the binding interface," Proteins: Structure, Function, and Bioinformatics, vol. 60, pp. 644-657, 2005.
    • (2005) Proteins: Structure, Function, and Bioinformatics , vol.60 , pp. 644-657
    • Green, D.F.1    Tidor, B.2
  • 28
    • 33646106797 scopus 로고    scopus 로고
    • Optimal charges in lead progression: A structure-based neuraminidase case study
    • K. A. Armstrong, B. Tidor, and A. C. Cheng, "Optimal charges in lead progression: A structure-based neuraminidase case study," Journal of Medicinal Chemistry, vol. 49, pp. 2470-2477, 2006.
    • (2006) Journal of Medicinal Chemistry , vol.49 , pp. 2470-2477
    • Armstrong, K.A.1    Tidor, B.2    Cheng, A.C.3
  • 29
    • 33846254079 scopus 로고    scopus 로고
    • Sensitivity analysis and charge-optimization for flexible ligands: Applicability to lead optimization
    • M. K. Gilson, "Sensitivity analysis and charge-optimization for flexible ligands: Applicability to lead optimization," Journal of Chemical Theory and Computation, vol. 2, no. 2, pp. 259-270, 2006.
    • (2006) Journal of Chemical Theory and Computation , vol.2 , Issue.2 , pp. 259-270
    • Gilson, M.K.1
  • 30
    • 0037621429 scopus 로고    scopus 로고
    • Charge optimization increases the potency and selectivity of a chorismate mutase inhibitor
    • A. Mandal and D. Hilvert, "Charge optimization increases the potency and selectivity of a chorismate mutase inhibitor," Journal of the American Chemical Society, vol. 125, no. 19, pp. 5598-5599, 2003.
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.19 , pp. 5598-5599
    • Mandal, A.1    Hilvert, D.2
  • 31
    • 33644934079 scopus 로고    scopus 로고
    • Parallel Lagrange-Newton-Krylov-Schur methods for PDE-constrained optimization. Part I: The Krylov-Schur solver
    • G. Biros and O. Ghattas, "Parallel Lagrange-Newton-Krylov-Schur methods for PDE-constrained optimization. Part I: the Krylov-Schur solver," SIAM Journal of Scientific Computing, vol. 27, no. 2, pp. 687-713, 2005.
    • (2005) SIAM Journal of Scientific Computing , vol.27 , Issue.2 , pp. 687-713
    • Biros, G.1    Ghattas, O.2
  • 35
    • 0022964504 scopus 로고
    • Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification
    • I. Klapper, R. Hagstrom, R. Fine, K. Sharp, and B. Honig, "Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: Effects of ionic strength and amino-acid modification," Proteins: Structure, Function, Genetics, vol. 1, pp. 47-59, 1986.
    • (1986) Proteins: Structure, Function, Genetics , vol.1 , pp. 47-59
    • Klapper, I.1    Hagstrom, R.2    Fine, R.3    Sharp, K.4    Honig, B.5
  • 36
    • 0023779259 scopus 로고
    • Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
    • M. K. Gilson and B. Honig, "Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis," Proteins: Structure, Function, Genetics, vol. 4, pp. 7-18, 1988.
    • (1988) Proteins: Structure, Function, Genetics , vol.4 , pp. 7-18
    • Gilson, M.K.1    Honig, B.2
  • 37
    • 0035913537 scopus 로고    scopus 로고
    • Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
    • W. Rocchia, E. Alexov, and B. Honig, "Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions," Journal of Physical Chemistry B, vol. 105, pp. 6507-6514, 2001.
    • (2001) Journal of Physical Chemistry B , vol.105 , pp. 6507-6514
    • Rocchia, W.1    Alexov, E.2    Honig, B.3
  • 38
    • 0041135034 scopus 로고
    • Multilevel methods for the Poisson-Boltzmann equation,
    • Ph.D. dissertation, Univ. of Ill. at Urbana-Champaign
    • M. J. Holst, "Multilevel methods for the Poisson-Boltzmann equation," Ph.D. dissertation, Univ. of Ill. at Urbana-Champaign, 1993.
    • (1993)
    • Holst, M.J.1
  • 40
    • 0001300681 scopus 로고
    • Theory of the Poisson Green's-function for discontinuous dielectric media with an application to protein biophysics
    • P. B. Shaw, "Theory of the Poisson Green's-function for discontinuous dielectric media with an application to protein biophysics," Physical Review A, vol. 32, no. 4, pp. 2476-2487, 1985.
    • (1985) Physical Review A , vol.32 , Issue.4 , pp. 2476-2487
    • Shaw, P.B.1
  • 41
    • 0022429751 scopus 로고
    • A new method for computing the macromolecular electric-potential
    • R. J. Zauhar and R. S. Morgan, "A new method for computing the macromolecular electric-potential," Journal of Molecular Biology, vol. 186, no. 4, pp. 815-820, 1985.
    • (1985) Journal of Molecular Biology , vol.186 , Issue.4 , pp. 815-820
    • Zauhar, R.J.1    Morgan, R.S.2
  • 42
    • 84962478456 scopus 로고
    • A boundary element method for molecular electrostatics with electrolyte effects
    • B. J. Yoon and A. M. Lenhoff, "A boundary element method for molecular electrostatics with electrolyte effects," Journal of Computational Chemistry, vol. 11, no. 9, pp. 1080-1086, 1990.
    • (1990) Journal of Computational Chemistry , vol.11 , Issue.9 , pp. 1080-1086
    • Yoon, B.J.1    Lenhoff, A.M.2
  • 43
    • 1942471026 scopus 로고    scopus 로고
    • Solution of the linearized Poisson-Boltzmann equation
    • D. M. Chipman, "Solution of the linearized Poisson-Boltzmann equation," Journal of Chemical Physics, vol. 120, no. 12, pp. 5566-5575, 2004.
    • (2004) Journal of Chemical Physics , vol.120 , Issue.12 , pp. 5566-5575
    • Chipman, D.M.1
  • 44
    • 84988110397 scopus 로고
    • The rigorous computation of the molecular electric potential
    • R. J. Zauhar and R. S. Morgan, "The rigorous computation of the molecular electric potential," Journal of Computational Chemistry, vol. 9, no. 2, pp. 171-187, 1988.
    • (1988) Journal of Computational Chemistry , vol.9 , Issue.2 , pp. 171-187
    • Zauhar, R.J.1    Morgan, R.S.2
  • 48
    • 0000048673 scopus 로고
    • GMRES: A generalized minimal residual algorithm for solving nonsymmetric linear systems
    • Y. Saad and M. Schultz, "GMRES: A generalized minimal residual algorithm for solving nonsymmetric linear systems," SIAM Journal of Scientific and Statistical Computing, vol. 7, pp. 856-869, 1986.
    • (1986) SIAM Journal of Scientific and Statistical Computing , vol.7 , pp. 856-869
    • Saad, Y.1    Schultz, M.2
  • 53
    • 0000151061 scopus 로고
    • Preconditioned, adaptive, multipole-accelerated iterative methods for three-dimensional first-kind integral equations of potential theory
    • K. Nabors, F. T. Korsmeyer, F. T. Leighton, and J. White, "Preconditioned, adaptive, multipole-accelerated iterative methods for three-dimensional first-kind integral equations of potential theory," SIAM Journal on Scientific Computing, vol. 15, no. 3, pp. 713-735, 1994.
    • (1994) SIAM Journal on Scientific Computing , vol.15 , Issue.3 , pp. 713-735
    • Nabors, K.1    Korsmeyer, F.T.2    Leighton, F.T.3    White, J.4
  • 58
    • 33644965417 scopus 로고    scopus 로고
    • Parallel Lagrange-Newton-Krylov-Schur methods for PDE-constrained optimization. Part II: The Lagrange-Newton solver and its application to optimal control of steady viscous flows
    • G. Biros and O. Ghattas, "Parallel Lagrange-Newton-Krylov-Schur methods for PDE-constrained optimization. Part II: the Lagrange-Newton solver and its application to optimal control of steady viscous flows," SIAM Journal of Scientific Computing, vol. 27, no. 2, pp. 714-739, 2005.
    • (2005) SIAM Journal of Scientific Computing , vol.27 , Issue.2 , pp. 714-739
    • Biros, G.1    Ghattas, O.2
  • 59
    • 0035665003 scopus 로고    scopus 로고
    • Preconditioned all-at-once methods for large, sparse parameter estimation problems
    • E. Haber and U. M. Ascher, "Preconditioned all-at-once methods for large, sparse parameter estimation problems," Inverse Problems, vol. 17, pp. 1847-1864, 2001.
    • (2001) Inverse Problems , vol.17 , pp. 1847-1864
    • Haber, E.1    Ascher, U.M.2
  • 61
    • 34547842573 scopus 로고    scopus 로고
    • Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces
    • No. 014701
    • J. P. Bardhan, M. D. Altman, D. J. Willis, S. M. Lippow, B. Tidor, and J. K. White, "Numerical integration techniques for curved-element discretizations of molecule-solvent interfaces," Journal of Chemical Physics, vol. 127, no. 014701, 2007.
    • (2007) Journal of Chemical Physics , vol.127
    • Bardhan, J.P.1    Altman, M.D.2    Willis, D.J.3    Lippow, S.M.4    Tidor, B.5    White, J.K.6
  • 62
    • 0043195299 scopus 로고    scopus 로고
    • Efficient techniques for wideband impedance extraction of complex 3-dimensional geometries,
    • Master's thesis, Massachusetts Institute of Technology
    • Z. Zhu, "Efficient techniques for wideband impedance extraction of complex 3-dimensional geometries," Master's thesis, Massachusetts Institute of Technology, 2002.
    • (2002)
    • Zhu, Z.1
  • 64
    • 16844371628 scopus 로고    scopus 로고
    • A fast direct solver for boundary integral equations in two dimensions
    • P. G. Martinsson and V. Rokhlin, "A fast direct solver for boundary integral equations in two dimensions," Journal of Computational Physics, vol. 205, pp. 1-23, 2005.
    • (2005) Journal of Computational Physics , vol.205 , pp. 1-23
    • Martinsson, P.G.1    Rokhlin, V.2
  • 65
    • 39549095132 scopus 로고    scopus 로고
    • personal communication
    • L. Greengard, personal communication.
    • Greengard, L.1
  • 66
    • 0026123179 scopus 로고
    • Inertia-controlling methods for general quadratic programming
    • P. E. Gill, W. Murray, M. A. Saunders, and M. H. Wright,"Inertia-controlling methods for general quadratic programming," SIAM Review, vol. 33, no. 1, pp. 1-36, 1991.
    • (1991) SIAM Review , vol.33 , Issue.1 , pp. 1-36
    • Gill, P.E.1    Murray, W.2    Saunders, M.A.3    Wright, M.H.4


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