-
1
-
-
0030945495
-
Incorporating protein conformational flexibility in the calculation of pH dependent protein properties
-
Alexov, E. and M. Gunner. 1997. Incorporating protein conformational flexibility in the calculation of pH dependent protein properties. Biophys. J. 75:2075-2093.
-
(1997)
Biophys. J.
, vol.75
, pp. 2075-2093
-
-
Alexov, E.1
Gunner, M.2
-
2
-
-
0025308916
-
Ion distributions around DNA and other cylindrical polyions: Theoretical descriptions and physical implications
-
Anderson, C. F., and M. T. Record. 1990. Ion distributions around DNA and other cylindrical polyions: theoretical descriptions and physical implications. Annu. Rev. Biophys. Biophys. Chem. 19:423-465.
-
(1990)
Annu. Rev. Biophys. Biophys. Chem.
, vol.19
, pp. 423-465
-
-
Anderson, C.F.1
Record, M.T.2
-
3
-
-
0017836325
-
Sodium-23 NMR studies of cation-DNA interactions
-
Anderson, C. F., M. T. Record, and P. A. Hart. 1978. Sodium-23 NMR studies of cation-DNA interactions. Biophys. Chem. 7:301-316.
-
(1978)
Biophys. Chem.
, vol.7
, pp. 301-316
-
-
Anderson, C.F.1
Record, M.T.2
Hart, P.A.3
-
4
-
-
0028305457
-
Prediction of the pH-dependent properties of proteins
-
Antosiewicz, J., J. A. McCammon, and M. K. Gilson. 1994. Prediction of the pH-dependent properties of proteins. J. Mol. Biol. 238:415-436.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 415-436
-
-
Antosiewicz, J.1
McCammon, J.A.2
Gilson, M.K.3
-
6
-
-
0030710155
-
Electrostatic and nonelectrostatic contributions to the binding free energies of anthracycline antibiotics to DNA
-
Baginski, M., F. Fogolari, and J. M. Briggs. 1997. Electrostatic and nonelectrostatic contributions to the binding free energies of anthracycline antibiotics to DNA. J. Mol. Biol. 274:253-267.
-
(1997)
J. Mol. Biol.
, vol.274
, pp. 253-267
-
-
Baginski, M.1
Fogolari, F.2
Briggs, J.M.3
-
7
-
-
0025381503
-
Sequence-selective, pH-dependent binding to DNA of benzophenanthridine alkaloids
-
Bajaj, N. P., M. J. McLean, M. J. Waring, and E. Smekal. 1990. Sequence-selective, pH-dependent binding to DNA of benzophenanthridine alkaloids. J. Mol. Recognit. 3:48-54.
-
(1990)
J. Mol. Recognit.
, vol.3
, pp. 48-54
-
-
Bajaj, N.P.1
McLean, M.J.2
Waring, M.J.3
Smekal, E.4
-
8
-
-
0026657433
-
Refined 1.8 Å crystal structure of the λ repressor-operator complex
-
Beamer, L. J., and C. O. Pabo. 1992. Refined 1.8 Å crystal structure of the λ repressor-operator complex. J. Mol. Biol. 227:177-196.
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 177-196
-
-
Beamer, L.J.1
Pabo, C.O.2
-
9
-
-
0025021874
-
A demonstration of the intrinsic importance of stabilizing hydrophobic binding and non-covalent van der Waals contacts dominant in the non-covalent CC-1065/B-DNA binding
-
Boger, D. L., B. J. Invergo, R. S. Coleman, H. Zarrinmayer, P. A. Kilos, S. A. Thompson, T. Leong, and L. W. McLaughlin. 1990. A demonstration of the intrinsic importance of stabilizing hydrophobic binding and non-covalent van der Waals contacts dominant in the non-covalent CC-1065/B-DNA binding. Chem. Biol. Interact. 73:29-52.
-
(1990)
Chem. Biol. Interact.
, vol.73
, pp. 29-52
-
-
Boger, D.L.1
Invergo, B.J.2
Coleman, R.S.3
Zarrinmayer, H.4
Kilos, P.A.5
Thompson, S.A.6
Leong, T.7
McLaughlin, L.W.8
-
10
-
-
0030961726
-
Entropy in protein folding and in protein-protein interactions
-
Brady, G. P., and K. A. Sharp. 1997. Entropy in protein folding and in protein-protein interactions. Curr. Opin. Struct. Biol. 7:215-221.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 215-221
-
-
Brady, G.P.1
Sharp, K.A.2
-
11
-
-
84986512474
-
CHARMM: A program for macromolecular energy minimization and dynamic calculations
-
Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: a program for macromolecular energy minimization and dynamic calculations. J. Comp. Chem. 4:187-217.
-
(1983)
J. Comp. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
12
-
-
0031249752
-
Monovalent and divalent salt effects on electrostatic free energies defined by the nonlinear Poisson-Boltzmann equation: Application to DNA binding reactions
-
Chen, S. W., and B. Honig. 1997. Monovalent and divalent salt effects on electrostatic free energies defined by the nonlinear Poisson-Boltzmann equation: application to DNA binding reactions. J. Phys. Chem. B. 101:9113-9118.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 9113-9118
-
-
Chen, S.W.1
Honig, B.2
-
13
-
-
0025835228
-
Evidence for hydrophobic interaction between calicheamicin and DNA
-
Ding, W.-D., and G. A. Ellestad. 1991. Evidence for hydrophobic interaction between calicheamicin and DNA. J. Am. Chem. Soc. 113: 6617-6620.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 6617-6620
-
-
Ding, W.-D.1
Ellestad, G.A.2
-
14
-
-
0024745871
-
The price of lost freedom: Entropy of bimolecular complex formation
-
Finkelstein, A. V., and J. Janin. 1989. The price of lost freedom: entropy of bimolecular complex formation. Protein Eng. 3:1-3.
-
(1989)
Protein Eng.
, vol.3
, pp. 1-3
-
-
Finkelstein, A.V.1
Janin, J.2
-
15
-
-
0029118487
-
A free energy analysis of nucleic acid base stacking in aqueous solution
-
Friedman, R., and B. Honig. 1995. A free energy analysis of nucleic acid base stacking in aqueous solution. Biophys. J. 69:1528-1535.
-
(1995)
Biophys. J.
, vol.69
, pp. 1528-1535
-
-
Friedman, R.1
Honig, B.2
-
16
-
-
0031008575
-
On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions
-
Froloff, N., A. Windemuth, and B. Honig. 1997. On the calculation of binding free energies using continuum methods: application to MHC class I protein-peptide interactions. Protein Sci. 6:1293-1301.
-
(1997)
Protein Sci.
, vol.6
, pp. 1293-1301
-
-
Froloff, N.1
Windemuth, A.2
Honig, B.3
-
18
-
-
0031058541
-
The statistical-thermodynamic basis for computation of binding affinities: A critical review
-
Gilson, M. K., J. A. Given, B. L. Bush, and J. A. McCammon. 1997. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys. J. 72:1047-1069.
-
(1997)
Biophys. J.
, vol.72
, pp. 1047-1069
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
19
-
-
0022816745
-
The dielectric constant of a folded protein
-
Gilson, M. K., and B. H. Honig. 1986. The dielectric constant of a folded protein. Biopolymers. 25:2097-2119.
-
(1986)
Biopolymers
, vol.25
, pp. 2097-2119
-
-
Gilson, M.K.1
Honig, B.H.2
-
20
-
-
0023779259
-
Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
-
Gilson, M. K., and B. Honig. 1988. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins Struct. Funct. Genet. 4:7-18.
-
(1988)
Proteins Struct. Funct. Genet.
, vol.4
, pp. 7-18
-
-
Gilson, M.K.1
Honig, B.2
-
21
-
-
0021813940
-
On the calculation of electrostatic interactions in proteins
-
Gilson, M. K., A. Rashin, R. Fine, and B. Honig. 1985. On the calculation of electrostatic interactions in proteins. J. Mol. Biol. 183:503-516.
-
(1985)
J. Mol. Biol.
, vol.183
, pp. 503-516
-
-
Gilson, M.K.1
Rashin, A.2
Fine, R.3
Honig, B.4
-
22
-
-
84988087911
-
Calculating the electrostatic potential of molecules in solution: Method and error assessment
-
Gilson, M. K., K. A. Sharp, and B. H. Honig. 1988. Calculating the electrostatic potential of molecules in solution: method and error assessment. J. Comput. Chem. 9:327-335.
-
(1988)
J. Comput. Chem.
, vol.9
, pp. 327-335
-
-
Gilson, M.K.1
Sharp, K.A.2
Honig, B.H.3
-
23
-
-
0027935845
-
A negative electrostatic determinant mediates the association between the Escherichia coli trp repressor and its operator DNA
-
Guenot, J., R. J. Fletterick, and P. A. Kollman. 1994. A negative electrostatic determinant mediates the association between the Escherichia coli trp repressor and its operator DNA. Protein Sci. 3:1276-1285.
-
(1994)
Protein Sci.
, vol.3
, pp. 1276-1285
-
-
Guenot, J.1
Fletterick, R.J.2
Kollman, P.A.3
-
24
-
-
0024378717
-
Role of the hydrophobic effect in stability of site-specific protein-DNA complexes
-
Ha, J.-H., R. S. Spolar, and M. T. Record. 1989. Role of the hydrophobic effect in stability of site-specific protein-DNA complexes. J. Mol. Biol. 209:801-816.
-
(1989)
J. Mol. Biol.
, vol.209
, pp. 801-816
-
-
Ha, J.-H.1
Spolar, R.S.2
Record, M.T.3
-
25
-
-
0028204490
-
Do salt bridges stabilize proteins? A continuum electrostatic analysis
-
Hendsch, Z. S., and B. Tidor. 1994. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 3:211-226.
-
(1994)
Protein Sci.
, vol.3
, pp. 211-226
-
-
Hendsch, Z.S.1
Tidor, B.2
-
26
-
-
33751385054
-
Macroscopic models of aqueous solutions: Biological and chemical application
-
Honig, B., K. Sharp, and A. Yang. 1993. Macroscopic models of aqueous solutions: biological and chemical application. J. Phys. Chem. 97: 1101-1109.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 1101-1109
-
-
Honig, B.1
Sharp, K.2
Yang, A.3
-
27
-
-
0001739390
-
A theoretical study of polyelectrolyte effects in protein-DNA interactions: Monte Carlo free energy simulations on the ion atmosphere contribution to the thermodynamics of λ repressor-operator complex formation
-
Jayaram, B., F. M. DiCapua, and D. L. Beveridge. 1991. A theoretical study of polyelectrolyte effects in protein-DNA interactions: Monte Carlo free energy simulations on the ion atmosphere contribution to the thermodynamics of λ repressor-operator complex formation. J. Am. Chem. Soc. 113:5211-5215.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 5211-5215
-
-
Jayaram, B.1
DiCapua, F.M.2
Beveridge, D.L.3
-
28
-
-
0024580271
-
The electrostatic potential of DNA
-
Jayaram, B., K. A. Sharp, and B. Honig. 1989. The electrostatic potential of DNA. Biopolymers. 28:975-993.
-
(1989)
Biopolymers
, vol.28
, pp. 975-993
-
-
Jayaram, B.1
Sharp, K.A.2
Honig, B.3
-
29
-
-
0025444642
-
Monte Carlo simulation studies on the structure of the counterion atmosphere of B-DNA. Variations on the primitive dielectric model
-
Jayaram, B., S. Swaminathan, D. L. Beveridge, K. A. Sharp, and B. Honig. 1990. Monte Carlo simulation studies on the structure of the counterion atmosphere of B-DNA. Variations on the primitive dielectric model. Macromolecules. 23:3156-3165.
-
(1990)
Macromolecules
, vol.23
, pp. 3156-3165
-
-
Jayaram, B.1
Swaminathan, S.2
Beveridge, D.L.3
Sharp, K.A.4
Honig, B.5
-
30
-
-
0021100513
-
Coordinate ion pair formation between EcoRI endonuclease and DNA
-
Jen-Jacobsen, L., M. Kurpiewski, D. Lesser, J. Grable, H. W. Boyer, J. M. Rosenberg, and P. J. Greene. 1983. Coordinate ion pair formation between EcoRI endonuclease and DNA. J. Biol. Chem. 258: 14638-14646.
-
(1983)
J. Biol. Chem.
, vol.258
, pp. 14638-14646
-
-
Jen-Jacobsen, L.1
Kurpiewski, M.2
Lesser, D.3
Grable, J.4
Boyer, H.W.5
Rosenberg, J.M.6
Greene, P.J.7
-
31
-
-
33645941402
-
The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin
-
Jorgensen, W. L., and J. Tirado-Rives. 1988. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1657-1666.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
32
-
-
0022964504
-
Focusing of electric fields in the active site of CuZn superoxide dismutase: Effects of ionic strength and amino acid modification
-
Klapper, I., R. Hagstrom, R. Fine, K. Sharp, and B. Honig. 1986. Focusing of electric fields in the active site of CuZn superoxide dismutase: effects of ionic strength and amino acid modification. Proteins Struct. Funct. Genet. 1:47-59.
-
(1986)
Proteins Struct. Funct. Genet.
, vol.1
, pp. 47-59
-
-
Klapper, I.1
Hagstrom, R.2
Fine, R.3
Sharp, K.4
Honig, B.5
-
33
-
-
0026717535
-
Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: A sliding DNA clamp
-
Kong, X. P., R. Onrust, M. O'Donnell, and J. Kuriyan. 1992. Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell. 69:425-437.
-
(1992)
Cell
, vol.69
, pp. 425-437
-
-
Kong, X.P.1
Onrust, R.2
O'Donnell, M.3
Kuriyan, J.4
-
34
-
-
0028283502
-
A thermodynamic study of the trp repressor-operator interaction
-
Ladbury, J. E., J. G. Wright, J. M. Sturtevant, and P. B. Sigler. 1994. A thermodynamic study of the trp repressor-operator interaction. J. Mol. Biol. 238:669-681.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 669-681
-
-
Ladbury, J.E.1
Wright, J.G.2
Sturtevant, J.M.3
Sigler, P.B.4
-
35
-
-
0027241925
-
Thermodynamics of the glucocorticoid receptor-DNA interaction: Binding of wild-type GR DBD to different response elements
-
Lundback, T., C. Cairns, J.-A. Gustafsson, J. Carlstedt-Duke, and T. Hard. 1993. Thermodynamics of the glucocorticoid receptor-DNA interaction: binding of wild-type GR DBD to different response elements. Biochemistry. 32:5074-5082.
-
(1993)
Biochemistry
, vol.32
, pp. 5074-5082
-
-
Lundback, T.1
Cairns, C.2
Gustafsson, J.-A.3
Carlstedt-Duke, J.4
Hard, T.5
-
36
-
-
20544473509
-
Limiting laws and counterion condensation in polyelectrolyte solutions. II. Self-diffusion of the small ions
-
Manning, G. S. 1969. Limiting laws and counterion condensation in polyelectrolyte solutions. II. Self-diffusion of the small ions. J. Chem. Phys. 51:934-938.
-
(1969)
J. Chem. Phys.
, vol.51
, pp. 934-938
-
-
Manning, G.S.1
-
37
-
-
0031547966
-
Electrostatic complementarity at protein/protein interfaces
-
McCoy, A. J., V. C. Epa, and P. M. Colman. 1997. Electrostatic complementarity at protein/protein interfaces. J. Mol. Biol. 268:570-584.
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 570-584
-
-
McCoy, A.J.1
Epa, V.C.2
Colman, P.M.3
-
38
-
-
0028239626
-
Salt effects on protein-DNA interactions: The λcI repressor and EcoRI endonuclease
-
Misra, V. K., J. L. Hecht, K. A. Sharp, R. A. Friedman, and B. Honig. 1994a. Salt effects on protein-DNA interactions: the λcI repressor and EcoRI endonuclease. J. Mol. Biol. 238:264-280.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 264-280
-
-
Misra, V.K.1
Hecht, J.L.2
Sharp, K.A.3
Friedman, R.A.4
Honig, B.5
-
39
-
-
0029047968
-
On the magnitude of the electrostatic contribution to ligand-DNA interactions
-
Misra, V. K., and B. Honig. 1995. On the magnitude of the electrostatic contribution to ligand-DNA interactions. Proc. Natl. Acad. Sci. USA. 92:4691-4695.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 4691-4695
-
-
Misra, V.K.1
Honig, B.2
-
40
-
-
0030032805
-
The electrostatic contribution to the B to Z transition of DNA
-
Misra, V. K., and B. Honig. 1996. The electrostatic contribution to the B to Z transition of DNA. Biochemistry. 35:1115-1124.
-
(1996)
Biochemistry
, vol.35
, pp. 1115-1124
-
-
Misra, V.K.1
Honig, B.2
-
41
-
-
0028246710
-
Salt effects on ligand-DNA binding: Minor groove binding antibiotics
-
Misra, V. K., K. A. Sharp, R. A. Friedman, and B. Honig. 1994b. Salt effects on ligand-DNA binding: minor groove binding antibiotics. J. Mol. Biol. 238:245-263.
-
(1994)
J. Mol. Biol.
, vol.238
, pp. 245-263
-
-
Misra, V.K.1
Sharp, K.A.2
Friedman, R.A.3
Honig, B.4
-
42
-
-
0027937135
-
Structure of an immunoglobulin Fab fragment specific for triple-stranded DNA
-
Mol, C. D., A. K. Muir, M. Cygler, J. S. Lee, and W. F. Anderson. 1994a. Structure of an immunoglobulin Fab fragment specific for triple-stranded DNA. J. Biol. Chem. 269:3615-3622.
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 3615-3622
-
-
Mol, C.D.1
Muir, A.K.2
Cygler, M.3
Lee, J.S.4
Anderson, W.F.5
-
43
-
-
0027994359
-
Structure of an immunoglobulin Fab fragment specific for poly(dG) · poly(dC)
-
Mol, C. D., A. K. Muir, J. S. Lee, and W. F. Anderson. 1994b. Structure of an immunoglobulin Fab fragment specific for poly(dG) · poly(dC). J. Biol. Chem. 269:3605-3614.
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 3605-3614
-
-
Mol, C.D.1
Muir, A.K.2
Lee, J.S.3
Anderson, W.F.4
-
44
-
-
0022129542
-
Lambda repressor mutations that increase the affinity and specificity of operator binding
-
Nelson, H. C. M., and S. T. Sauer. 1985. Lambda repressor mutations that increase the affinity and specificity of operator binding. Cell. 42: 549-558.
-
(1985)
Cell
, vol.42
, pp. 549-558
-
-
Nelson, H.C.M.1
Sauer, S.T.2
-
45
-
-
84986486656
-
A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
-
Nicholls, A., and B. Honig. 1991. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comp. Chem. 12:435-445.
-
(1991)
J. Comp. Chem.
, vol.12
, pp. 435-445
-
-
Nicholls, A.1
Honig, B.2
-
46
-
-
0026319199
-
Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
-
Nicholls, A., K. A. Sharp, and B. Honig. 1991. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11:281-296.
-
(1991)
Proteins Struct. Funct. Genet.
, vol.11
, pp. 281-296
-
-
Nicholls, A.1
Sharp, K.A.2
Honig, B.3
-
47
-
-
84988103838
-
Energy functions for energy minimization and dynamics of nucleic acids
-
Nilsson, L., and M. Karplus. 1984. Energy functions for energy minimization and dynamics of nucleic acids. J. Comp. Chem. 1:591-616.
-
(1984)
J. Comp. Chem.
, vol.1
, pp. 591-616
-
-
Nilsson, L.1
Karplus, M.2
-
48
-
-
0028297873
-
Linkage of pH, anion and cation effects in protein-nucleic acid equilibria. Escherichia coli SSB protein-single stranded nucleic acid interactions
-
Overman, L. B., and T. M. Lohman. 1994. Linkage of pH, anion and cation effects in protein-nucleic acid equilibria. Escherichia coli SSB protein-single stranded nucleic acid interactions. J. Mol. Biol. 236:165-178.
-
(1994)
J. Mol. Biol.
, vol.236
, pp. 165-178
-
-
Overman, L.B.1
Lohman, T.M.2
-
49
-
-
0028773287
-
Electrostatic activation of the Escherichia coli methionine repressor
-
Phillips, K., and S. E. V. Phillips. 1994. Electrostatic activation of the Escherichia coli methionine repressor. Structure. 2:209-316.
-
(1994)
Structure
, vol.2
, pp. 209-316
-
-
Phillips, K.1
Phillips, S.E.V.2
-
50
-
-
0024419731
-
Cooperative tandem binding of met repressor of Escherichia coli
-
Phillips, S. E. V., I. Manfield, I. Parsons, B. E. Davidson, J. B. Rafferty, W. S. Somers, D. Margarita, G. N. Cohen, I. Saint-Girons, and P. G. Stockley. 1989. Cooperative tandem binding of met repressor of Escherichia coli. Nature. 341:711-720.
-
(1989)
Nature
, vol.341
, pp. 711-720
-
-
Phillips, S.E.V.1
Manfield, I.2
Parsons, I.3
Davidson, B.E.4
Rafferty, J.B.5
Somers, W.S.6
Margarita, D.7
Cohen, G.N.8
Saint-Girons, I.9
Stockley, P.G.10
-
51
-
-
0027166270
-
Empirical scale of side-chain conformational entropy in protein folding
-
Pickett, S. D., and M. J. E. Sternberg. 1993. Empirical scale of side-chain conformational entropy in protein folding. J. Mol. Biol. 231:825-839.
-
(1993)
J. Mol. Biol.
, vol.231
, pp. 825-839
-
-
Pickett, S.D.1
Sternberg, M.J.E.2
-
52
-
-
0025728614
-
OPLS potential functions for nucleotide bases. Relative association constants of hydrogen-bonded base pairs in chloroform
-
Pranata, J., S. G. Wierschke, W. L. Jorgensen. 1991. OPLS potential functions for nucleotide bases. Relative association constants of hydrogen-bonded base pairs in chloroform. J. Am. Chem. Soc. 113: 2810-2819.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 2810-2819
-
-
Pranata, J.1
Wierschke, S.G.2
Jorgensen, W.L.3
-
53
-
-
0017820499
-
Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity
-
Record, M. T., C. F. Anderson, and T. M. Lohman. 1978. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q. Rev. Biophys. 11: 103-178.
-
(1978)
Q. Rev. Biophys.
, vol.11
, pp. 103-178
-
-
Record, M.T.1
Anderson, C.F.2
Lohman, T.M.3
-
54
-
-
0026323912
-
Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA
-
Record, M. T., J.-H. Ha, and M. A. Fisher. 1991. Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA. Methods Enzymol. 208: 291-343.
-
(1991)
Methods Enzymol.
, vol.208
, pp. 291-343
-
-
Record, M.T.1
Ha, J.-H.2
Fisher, M.A.3
-
55
-
-
0000058799
-
λ repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically
-
Sarai, A., and Y. Takeda. 1989. λ repressor recognizes the approximately 2-fold symmetric half-operator sequences asymmetrically. Proc. Natl. Acad. Sci. USA. 86:6513-6517.
-
(1989)
Proc. Natl. Acad. Sci. USA
, vol.86
, pp. 6513-6517
-
-
Sarai, A.1
Takeda, Y.2
-
56
-
-
0025330003
-
Lambda repressor: A model system for understanding protein-DNA interactions and protein stability
-
Sauer, R. T., S. R. Jordan, and C. O. Pabo. 1990. Lambda repressor: a model system for understanding protein-DNA interactions and protein stability. Adv. Protein Chem. 40:1-61.
-
(1990)
Adv. Protein Chem.
, vol.40
, pp. 1-61
-
-
Sauer, R.T.1
Jordan, S.R.2
Pabo, C.O.3
-
57
-
-
0025914242
-
Crystal structure of a CAP-DNA complex: The DNA is bent by 90 degrees
-
Schultz, S. C., G. C. Shields, and T. A. Steitz. 1991. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science. 253: 1001-1007.
-
(1991)
Science
, vol.253
, pp. 1001-1007
-
-
Schultz, S.C.1
Shields, G.C.2
Steitz, T.A.3
-
58
-
-
0025315476
-
Proton-linked contributions to site-specific interactions of lambda cI repressor and OR
-
Senear, D. F., and G. K. Ackers. 1990. Proton-linked contributions to site-specific interactions of lambda cI repressor and OR. Biochemistry. 29:6568-6577.
-
(1990)
Biochemistry
, vol.29
, pp. 6568-6577
-
-
Senear, D.F.1
Ackers, G.K.2
-
59
-
-
0025741694
-
Comparison of operator-specific and nonspecific DNA binding of the lambda cI repressor: [KCl] and pH effects
-
Senear, D. F., and R. Batey. 1991. Comparison of operator-specific and nonspecific DNA binding of the lambda cI repressor: [KCl] and pH effects. Biochemistry. 30:6677-6688.
-
(1991)
Biochemistry
, vol.30
, pp. 6677-6688
-
-
Senear, D.F.1
Batey, R.2
-
60
-
-
0028315988
-
Determinants of repressor/operator recognition from the structure of the trp operator binding site
-
Shakked, Z., G. Guzikevich-Guerstein, F. Frolow, D. Rabinovich, A. Joachimiak, and P. B. Sigler. 1994. Determinants of repressor/operator recognition from the structure of the trp operator binding site. Nature. 368:469-473.
-
(1994)
Nature
, vol.368
, pp. 469-473
-
-
Shakked, Z.1
Guzikevich-Guerstein, G.2
Frolow, F.3
Rabinovich, D.4
Joachimiak, A.5
Sigler, P.B.6
-
61
-
-
0029068766
-
Polyelectrolyte electrostatics: Salt dependence, entropic, and enthalpic contributions to free energy in the nonlinear Poisson-Boltzmann model
-
Sharp, K. A. 1995. Polyelectrolyte electrostatics: salt dependence, entropic, and enthalpic contributions to free energy in the nonlinear Poisson-Boltzmann model. Biopolymers. 36:227-243.
-
(1995)
Biopolymers
, vol.36
, pp. 227-243
-
-
Sharp, K.A.1
-
62
-
-
33751552991
-
Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation
-
Sharp, K. A., and B. Honig. 1990a. Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation. J. Phys. Chem. 94: 7684-7692.
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 7684-7692
-
-
Sharp, K.A.1
Honig, B.2
-
63
-
-
0025283002
-
Electrostatic interactions in macromolecules: Theory and applications
-
Sharp, K. A., and B. Honig. 1990b. Electrostatic interactions in macromolecules: theory and applications. Annu. Rev. Biophys. Biophys. Chem. 19:301-332.
-
(1990)
Annu. Rev. Biophys. Biophys. Chem.
, vol.19
, pp. 301-332
-
-
Sharp, K.A.1
Honig, B.2
-
64
-
-
0026416668
-
Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects
-
Sharp, K. A., A. Nicholls, R. F. Fine, and B. Honig. 1991. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science. 252:106-109.
-
(1991)
Science
, vol.252
, pp. 106-109
-
-
Sharp, K.A.1
Nicholls, A.2
Fine, R.F.3
Honig, B.4
-
65
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
Sitkoff, D., K. A. Sharp, and B. Honig. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 98:1978-1988.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
66
-
-
23444450909
-
Coupling of local folding to site-specific binding of proteins to DNA
-
Spolar, R. S., and M. T. J. Record. 1994. Coupling of local folding to site-specific binding of proteins to DNA. Science. 263:777-784.
-
(1994)
Science
, vol.263
, pp. 777-784
-
-
Spolar, R.S.1
Record, M.T.J.2
-
67
-
-
0014718113
-
Protein denaturation, part C
-
Tanford, C. 1970. Protein denaturation, part C. Adv. Protein Chem. 24: 1-95.
-
(1970)
Adv. Protein Chem.
, vol.24
, pp. 1-95
-
-
Tanford, C.1
-
68
-
-
0020962967
-
Dynamics of DNA oligomers
-
Tidor, B., K. K. Irikura, B. R. Brooks, and M. Karplus. 1983. Dynamics of DNA oligomers. J. Biomol. Struct. Dyn. 1:231-252.
-
(1983)
J. Biomol. Struct. Dyn.
, vol.1
, pp. 231-252
-
-
Tidor, B.1
Irikura, K.K.2
Brooks, B.R.3
Karplus, M.4
-
69
-
-
0023461357
-
Electrostatic calculations and model-building suggest that DNA bound to CAP is sharply bent
-
Warwicker, J., B. P. Engelman, and T. A. Steitz. 1987. Electrostatic calculations and model-building suggest that DNA bound to CAP is sharply bent. Proteins. 2:283-289.
-
(1987)
Proteins
, vol.2
, pp. 283-289
-
-
Warwicker, J.1
Engelman, B.P.2
Steitz, T.A.3
-
70
-
-
0022368152
-
Electrostatic field of the large fragment of Escherichia coli DNA polymerase I
-
Warwicker, J., D. Ollis, F. M. Richards, and T. A. Steitz. 1985. Electrostatic field of the large fragment of Escherichia coli DNA polymerase I. J. Mol. Biol. 186:645-649.
-
(1985)
J. Mol. Biol.
, vol.186
, pp. 645-649
-
-
Warwicker, J.1
Ollis, D.2
Richards, F.M.3
Steitz, T.A.4
-
71
-
-
84988053694
-
An all atom force field for simulations of proteins and nucleic acids
-
Weiner, S. J., P. A. Kollman, D. T. Nguyen, and D. A. Case. 1986. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 7:230-252.
-
(1986)
J. Comput. Chem.
, vol.7
, pp. 230-252
-
-
Weiner, S.J.1
Kollman, P.A.2
Nguyen, D.T.3
Case, D.A.4
-
73
-
-
0028147373
-
A computer-assisted analysis of conserved residues in the three-dimensional structures of the polymerase domains of Escherichia coli DNA polymerase I and HIV-1 reverse transcriptase
-
Yadav, P. N., J. S. Yadav, E. Arnold, and M. J. Modak. 1994. A computer-assisted analysis of conserved residues in the three-dimensional structures of the polymerase domains of Escherichia coli DNA polymerase I and HIV-1 reverse transcriptase. J. Biol. Chem. 269:716-720.
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 716-720
-
-
Yadav, P.N.1
Yadav, J.S.2
Arnold, E.3
Modak, M.J.4
-
74
-
-
0026439270
-
Binding of DNA to large fragment of DNA polymerase. I. Identification of strong and weak electrostatic forces and their biological implications
-
Yadav, P. N., J. S. Yadav, and M. J. Modak. 1992. Binding of DNA to large fragment of DNA polymerase. I. Identification of strong and weak electrostatic forces and their biological implications. J. Biomol. Struct. Dyn. 10:311-316.
-
(1992)
J. Biomol. Struct. Dyn.
, vol.10
, pp. 311-316
-
-
Yadav, P.N.1
Yadav, J.S.2
Modak, M.J.3
-
76
-
-
0027231258
-
On the pH dependence of protein stability
-
Yang, A.-S., and B. Honig. 1993. On the pH dependence of protein stability. J. Mol. Biol 231:459-474.
-
(1993)
J. Mol. Biol
, vol.231
, pp. 459-474
-
-
Yang, A.-S.1
Honig, B.2
-
77
-
-
0029148986
-
Dielectric response of triplex DNA in ionic solution from simulations
-
Yang, L., S. Weerasinghe, P. E. Smith, and B. M. Pettitt. 1995. Dielectric response of triplex DNA in ionic solution from simulations. Biophys. J. 69:1519-1527.
-
(1995)
Biophys. J.
, vol.69
, pp. 1519-1527
-
-
Yang, L.1
Weerasinghe, S.2
Smith, P.E.3
Pettitt, B.M.4
-
78
-
-
0026619551
-
Poisson-Boltzmann analysis of the λ repressor-operator interaction
-
Zacharias, M., B. A. Luty, M. E. Davis, and J. A. McCammon. 1992. Poisson-Boltzmann analysis of the λ repressor-operator interaction. Biophys. J. 3:1280-1285.
-
(1992)
Biophys. J.
, vol.3
, pp. 1280-1285
-
-
Zacharias, M.1
Luty, B.A.2
Davis, M.E.3
McCammon, J.A.4
|