journal article Jul 31, 2002

Introducing an Implicit Membrane in Generalized Born/Solvent Accessibility Continuum Solvent Models

View at Publisher Save 10.1021/jp020674r
Topics

No keywords indexed for this article. Browse by subject →

References
55
[1]
Schaefer M. Adv. Protein Chem. (1998)
[2]
Bashford D. J. Mol. Biol. (1992) 10.1016/0022-2836(92)91009-e
[3]
Bashford (1997) 10.1007/3-540-63827-x_66
[4]
Karshikoff A. J. Mol. Biol. (1994) 10.1006/jmbi.1994.1451
[5]
Im W. Comput. Phys. Commun. (1998)
[6]
Rocchia W. J. Phys. Chem. B (2001)
[7]
Semianalytical treatment of solvation for molecular mechanics and dynamics

W. Clark Still, Anna Tempczyk, Ronald C. Hawley et al.

Journal of the American Chemical Society 1990 10.1021/ja00172a038
[8]
Qiu D. J. Phys. Chem. (1997)
[9]
Dominy B. N. III J. Phys. Chem. B (1999)
[10]
Bursulaya B. D. III J. Phys. Chem. B (2000)
[11]
Schaefer M. Theor. Chem. Acc. (1999) 10.1007/s002140050429
[12]
General Semiempirical Quantum Mechanical Solvation Model for Nonpolar Solvation Free Energies. n-Hexadecane

David J. Giesen, Joey W. Storer, Christopher J. Cramer et al.

Journal of the American Chemical Society 1995 10.1021/ja00108a023
[13]
Modification of the Generalized Born Model Suitable for Macromolecules

Alexey Onufriev, Donald Bashford, David A. Case

The Journal of Physical Chemistry B 2000 10.1021/jp994072s
[14]
Zou X. J. Am. Chem. Soc. (1999)
[15]
Generalized Born Models of Macromolecular Solvation Effects

Donald Bashford, David A. Case

Annual Review of Physical Chemistry 2000 10.1146/annurev.physchem.51.1.129
[16]
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson et al.

Journal of Computational Chemistry 1983 10.1002/jcc.540040211
[17]
CHARMm c27b4 is the commercial version of CHARMM c27b4 distributed by Accelrys Inc., 2001.
[18]
Atomic solvation parameters applied to molecular dynamics of proteins in solution

Laura Wesson, David Eisenberg

Protein Science 1992 10.1002/pro.5560010204
[19]
Wiley D. C. J. Annu. Rev. Biochem. (1987) 10.1146/annurev.bi.56.070187.002053
[20]
Zhou Z. Biophys. J. (2000)
[21]
Bechor D. Biophys. J. (2001) 10.1016/s0006-3495(01)76045-6
[22]
Lee B. J. Mol. Biol. (1971)
[23]
Shaefer M. J. Phys. Chem. (1996)
[24]
Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

Gregory D. Hawkins, Christopher J. Cramer, Donald G. Truhlar

The Journal of Physical Chemistry 1996 10.1021/jp961710n
[25]
Scarsi M. J. Phys. Chem. (1997) 10.1021/jp9714227
[26]
Parsegian A Nature (1969) 10.1038/221844a0
[27]
Solvent accessible surface area and excluded volume in proteins

Timothy J. Richmond

Journal of Molecular Biology 1984 10.1016/0022-2836(84)90231-6
[28]
MEMBRANE PROTEIN FOLDING AND STABILITY: Physical Principles

Stephen H. White, William C. Wimley

Annual Review of Biophysics and Biomolecular Struc... 1999 10.1146/annurev.biophys.28.1.319
[29]
Structure of bacteriorhodopsin at 1.55 Å resolution

Hartmut Luecke, Brigitte Schobert, Hans-Thomas Richter et al.

Journal of Molecular Biology 1999 10.1006/jmbi.1999.3027
[30]
Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor

Krzysztof Palczewski, Takashi Kumasaka, Tetsuya Hori et al.

Science 2000 10.1126/science.289.5480.739
[31]
Spassov V. Z. J. Mol. Biol. (2001) 10.1006/jmbi.2001.4902
[32]
Neria E. J. Chem. Phys. (1996)
[33]
Sitkoff D. J. Phys. Chem. (1996) 10.1021/jp952986i
[34]
Bashford D. Biochemistry (1990) 10.1021/bi00496a010
[35]
Handbook FL (1986)
[36]
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

Jean-Paul Ryckaert, Giovanni Ciccotti, Herman J.C Berendsen

Journal of Computational Physics 1977 10.1016/0021-9991(77)90098-5
[37]
Wiener M. C. Biophys. J. (1992)
[38]
Membrane protein structure prediction

Gunnar von Heijne

Journal of Molecular Biology 1992 10.1016/0022-2836(92)90934-c
[39]
van Klompenburg W. EMBO J. (1997) 10.1093/emboj/16.14.4261
[40]
Stegman, T.; Helenius, A. InViral Fusion Mechanism; Benz, J., Ed.; CRC Press, Inc.  Boca Raton, FL, 1993; pp 89−111.
[41]
Macosko J. C. J. Mol. Biol. (1997) 10.1006/jmbi.1997.0931
[42]
Takahashi S. Biochemistry (1990) 10.1021/bi00478a022
[43]
Luneberg J. J Biol. Chem. (1995) 10.1074/jbc.270.46.27606
[44]
Han X. Biochemistry (1999)
[45]
Solvation energy in protein folding and binding

David Eisenberg, Andrew D. McLachlan

Nature 1986 10.1038/319199a0
[46]
A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation

Anthony Nicholls, Barry Honig

Journal of Computational Chemistry 1991 10.1002/jcc.540120405
[47]
Hol W. G. J. Nature (1978) 10.1038/273446a0
[48]
Spassov V. Z. Protein Sci. (1997)
[49]
Han X. Nat. Struct. Biol. (2001)
[50]
Ben-Tal N. Biophys. J. (1996)

Showing 50 of 55 references

Cited By
153
The Journal of Physical Chemistry B
Protein Science
Generalized Born Implicit Solvent Models for Biomolecules

Alexey V. Onufriev, David A. Case · 2019

Annual Review of Biophysics
Proteins: Structure, Function, and...
Theoretical Chemistry Accounts
Proteins: Structure, Function, and...
Metrics
153
Citations
55
References
Details
Published
Jul 31, 2002
Vol/Issue
106(34)
Pages
8726-8738
Cite This Article
Velin Z. Spassov, Lisa Yan, Sándor Szalma (2002). Introducing an Implicit Membrane in Generalized Born/Solvent Accessibility Continuum Solvent Models. The Journal of Physical Chemistry B, 106(34), 8726-8738. https://doi.org/10.1021/jp020674r