-
1
-
-
0036681440
-
Empirical relationships between protein structure and carboxyl pK(a) values in proteins
-
Forsyth WR, Antosiewiez JM, Robertson AD. Empirical relationships between protein structure and carboxyl pK(a) values in proteins. Proteins 2002;48:388-403.
-
(2002)
Proteins
, vol.48
, pp. 388-403
-
-
Forsyth, W.R.1
Antosiewiez, J.M.2
Robertson, A.D.3
-
2
-
-
0036783381
-
Variability in the pKa of histidine side-chains correlates with burial within proteins
-
Edgcomb SP, Murphy KP. Variability in the pKa of histidine side-chains correlates with burial within proteins. Proteins 2002; 49:1-6.
-
(2002)
Proteins
, vol.49
, pp. 1-6
-
-
Edgcomb, S.P.1
Murphy, K.P.2
-
3
-
-
0036001159
-
Structural basis of perturbed p(Ka) values of catalytic groups in enzyme active sites
-
Harris TK, Turner GJ. Structural basis of perturbed p(Ka) values of catalytic groups in enzyme active sites. IUBMB Life 2002;53:85-98.
-
(2002)
IUBMB Life
, vol.53
, pp. 85-98
-
-
Harris, T.K.1
Turner, G.J.2
-
4
-
-
0034855331
-
The determinants of alpha-amylase pH-activity profiles
-
Nielsen JE, Borchert TV, Vriend G. The determinants of alpha-amylase pH-activity profiles. Protein Eng 2001;14:505-512.
-
(2001)
Protein Eng
, vol.14
, pp. 505-512
-
-
Nielsen, J.E.1
Borchert, T.V.2
Vriend, G.3
-
5
-
-
0023660015
-
Electrostatic effects on modification of charged groups in the active-site cleft of subtilisin by protein engineering
-
Russell AJ, Thomas PG, Fersht AR. Electrostatic effects on modification of charged groups in the active-site cleft of subtilisin by protein engineering. J Mol Biol 1987;193:803-813.
-
(1987)
J Mol Biol
, vol.193
, pp. 803-813
-
-
Russell, A.J.1
Thomas, P.G.2
Fersht, A.R.3
-
6
-
-
0027257747
-
Long-range surface-charge charge interactions in proteins-comparison of experimental results with calculations from a theoretical method
-
Loewenthal R, Sancho J, Reinikainen T, Fersht AR. Long-range surface-charge charge interactions in proteins-comparison of experimental results with calculations from a theoretical method. J Mol Biol 1993;232:574-583.
-
(1993)
J Mol Biol
, vol.232
, pp. 574-583
-
-
Loewenthal, R.1
Sancho, J.2
Reinikainen, T.3
Fersht, A.R.4
-
7
-
-
0034636803
-
Insensitivity of perturbed carboxyl pK(a) values in the ovomucoid third domain to charge replacement at a neighboring residue
-
Forsyth WR, Robertson AD. Insensitivity of perturbed carboxyl pK(a) values in the ovomucoid third domain to charge replacement at a neighboring residue. Biochemistry 2000;39:8067-8072.
-
(2000)
Biochemistry
, vol.39
, pp. 8067-8072
-
-
Forsyth, W.R.1
Robertson, A.D.2
-
8
-
-
0037129945
-
Electrostatic interactions in ubiquitin: Stabilization of carboxylates by lysine amino groups
-
Sundd M, Iverson N, Ibarra-Molero B, Sanchez-Ruiz JM, Robertson AD. Electrostatic interactions in ubiquitin: stabilization of carboxylates by lysine amino groups. Biochemistry 2002;41:7586-7596.
-
(2002)
Biochemistry
, vol.41
, pp. 7586-7596
-
-
Sundd, M.1
Iverson, N.2
Ibarra-Molero, B.3
Sanchez-Ruiz, J.M.4
Robertson, A.D.5
-
9
-
-
2442429974
-
Role of microenvironments in modulating pKa shifts in proteins
-
Mehler EL, Fuxreiter M, Garcia-Moreno B. Role of microenvironments in modulating pKa shifts in proteins. Biophys J 2002;82: 1748.
-
(2002)
Biophys J
, vol.82
, pp. 1748
-
-
Mehler, E.L.1
Fuxreiter, M.2
Garcia-Moreno, B.3
-
10
-
-
0036681396
-
The role of hydrophobic microenvironments in modulating pK(a) shifts in proteins
-
Mehler EL, Fuxreiter M, Simon I, Garcia-Moreno EB. The role of hydrophobic microenvironments in modulating pK(a) shifts in proteins. Proteins 2002;48:283-292.
-
(2002)
Proteins
, vol.48
, pp. 283-292
-
-
Mehler, E.L.1
Fuxreiter, M.2
Simon, I.3
Garcia-Moreno, E.B.4
-
11
-
-
0033850087
-
High apparent dielectric constants in the interior of a protein reflect water penetration
-
Dwyer JJ, Gittis AG, Karp DA, Lattman EE, Spencer DS, Stites WE, Garcia-Moreno B. High apparent dielectric constants in the interior of a protein reflect water penetration. Biophys J 2000;79: 1610-1620.
-
(2000)
Biophys J
, vol.79
, pp. 1610-1620
-
-
Dwyer, J.J.1
Gittis, A.G.2
Karp, D.A.3
Lattman, E.E.4
Spencer, D.S.5
Stites, W.E.6
Garcia-Moreno, B.7
-
12
-
-
0034111423
-
The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase
-
Lambeir AM, Backmann J, Ruiz-Sanz J, Filimonov V, Nielsen JE, Kursula I, Norledge BV, Wierenga RK. The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase. Eur J Biochem 2000;267:2516-2524.
-
(2000)
Eur J Biochem
, vol.267
, pp. 2516-2524
-
-
Lambeir, A.M.1
Backmann, J.2
Ruiz-Sanz, J.3
Filimonov, V.4
Nielsen, J.E.5
Kursula, I.6
Norledge, B.V.7
Wierenga, R.K.8
-
13
-
-
0017292056
-
The alpha-helix as an electric macrodipole
-
Wada A. The alpha-helix as an electric macrodipole. Adv Biophys 1976;9:1-63.
-
(1976)
Adv Biophys
, vol.9
, pp. 1-63
-
-
Wada, A.1
-
14
-
-
0021978310
-
The role of the alpha-helix dipole in protein function and structure
-
Hol WGJ. The role of the alpha-helix dipole in protein function and structure. Prog Biophys Mol Biol 1985;45:149-195.
-
(1985)
Prog Biophys Mol Biol
, vol.45
, pp. 149-195
-
-
Hol, W.G.J.1
-
15
-
-
0024290472
-
Amino-acid preferences for specific locations at the ends of alpha-helices
-
Richardson JS, Richardson DC. Amino-acid preferences for specific locations at the ends of alpha-helices. Science 1988;240:1648-1652.
-
(1988)
Science
, vol.240
, pp. 1648-1652
-
-
Richardson, J.S.1
Richardson, D.C.2
-
16
-
-
0026590664
-
Histidine-residues at the N-termini and C-termini of alpha-helices-perturbed Pkas and protein stability
-
Sancho J, Serrano L, Fersht AR. Histidine-residues at the N-termini and C-termini of alpha-helices-perturbed Pkas and protein stability. Biochemistry 1992;31:2253-2258.
-
(1992)
Biochemistry
, vol.31
, pp. 2253-2258
-
-
Sancho, J.1
Serrano, L.2
Fersht, A.R.3
-
17
-
-
0028886558
-
Ionization of cysteine residues at the termini of model alpha-helical peptides-relevance to unusual thiol Pk(a) values in proteins of the thioredoxin family
-
Kortemme T, Creighton TE. Ionization of cysteine residues at the termini of model alpha-helical peptides-relevance to unusual thiol Pk(a) values in proteins of the thioredoxin family. J Mol Biol 1995;253:799-812.
-
(1995)
J Mol Biol
, vol.253
, pp. 799-812
-
-
Kortemme, T.1
Creighton, T.E.2
-
18
-
-
0000467270
-
Electrostatic basis of structure-function correlation in proteins
-
Warshel A. Electrostatic basis of structure-function correlation in proteins. Acc Chem Res 1981;14:284-290.
-
(1981)
Acc Chem Res
, vol.14
, pp. 284-290
-
-
Warshel, A.1
-
19
-
-
0025197061
-
pkas of ionizable groups in proteins - Atomic detail from a continuum electrostatic model
-
Bashford D, Karplus M. pkas of Ionizable groups in proteins - atomic detail from a continuum electrostatic model. Biochemistry 1990;29:10219-10225.
-
(1990)
Biochemistry
, vol.29
, pp. 10219-10225
-
-
Bashford, D.1
Karplus, M.2
-
20
-
-
0027563464
-
On the calculation of pkas in proteins
-
, Yang AS, Gunner MR, Sampogna R, Sharp K, Honig B. On the calculation of pkas in proteins. Proteins 1993;15:252-265.
-
(1993)
Proteins
, vol.15
, pp. 252-265
-
-
Yang, A.S.1
Gunner, M.R.2
Sampogna, R.3
Sharp, K.4
Honig, B.5
-
22
-
-
0000945505
-
Computing ionization states of proteins with a detailed charge model
-
Antosiewicz J, Briggs JM, Elcock AH, Gilson MK, McCammon JA. Computing ionization states of proteins with a detailed charge model. J Comput Chem 1996;17:1633-1644.
-
(1996)
J Comput Chem
, vol.17
, pp. 1633-1644
-
-
Antosiewicz, J.1
Briggs, J.M.2
Elcock, A.H.3
Gilson, M.K.4
McCammon, J.A.5
-
23
-
-
0000671518
-
Consistent calculations of pK(a)'s of ionizable residues in proteins: Semi-microscopic and microscopic approaches
-
Sham YY, Chu ZT, Warshel A. Consistent calculations of pK(a)'s of ionizable residues in proteins: semi-microscopic and microscopic approaches. J Phys Chem B 1997;101:4458-4472.
-
(1997)
J Phys Chem B
, vol.101
, pp. 4458-4472
-
-
Sham, Y.Y.1
Chu, Z.T.2
Warshel, A.3
-
24
-
-
0028169692
-
Intrinsic pkas of ionizable residues in proteins-an explicit solvent calculation for lysozyme
-
Delbuono GS, Figueirido FE, Levy RM. Intrinsic pkas of ionizable residues in proteins-an explicit solvent calculation for lysozyme. Proteins 1994;20:85-97.
-
(1994)
Proteins
, vol.20
, pp. 85-97
-
-
Delbuono, G.S.1
Figueirido, F.E.2
Levy, R.M.3
-
25
-
-
0023060081
-
Free-energy of charges in solvated proteins-microscopic calculations using a reversible charging process
-
Warshel A, Sussman F, King G. Free-energy of charges in solvated proteins-microscopic calculations using a reversible charging process. Biochemistry 1986;25:8368-8372.
-
(1986)
Biochemistry
, vol.25
, pp. 8368-8372
-
-
Warshel, A.1
Sussman, F.2
King, G.3
-
26
-
-
7044239742
-
Free-energy calculations-applications to chemical and biochemical phenomena
-
Kollman P. Free-energy calculations-applications to chemical and biochemical phenomena. Chem Rev 1993;93:2395-2417.
-
(1993)
Chem Rev
, vol.93
, pp. 2395-2417
-
-
Kollman, P.1
-
27
-
-
0033012333
-
A self-consistent, microenvironment modulated screened Coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins
-
Mehler EL, Guarnieri F. A self-consistent, microenvironment modulated screened Coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins. Biophys J 1999;77:3-22.
-
(1999)
Biophys J
, vol.77
, pp. 3-22
-
-
Mehler, E.L.1
Guarnieri, F.2
-
28
-
-
0032769471
-
A fast and simple method to calculate protonation states in proteins
-
Sandberg L, Edholm O. A fast and simple method to calculate protonation states in proteins. Proteins 1999;36:474-483.
-
(1999)
Proteins
, vol.36
, pp. 474-483
-
-
Sandberg, L.1
Edholm, O.2
-
29
-
-
0022522422
-
Calculation of electrostatic interactions in proteins
-
Matthew JB, Gurd FRN. Calculation of electrostatic interactions in proteins. Methods Enzymol 1986;130:413-436.
-
(1986)
Methods Enzymol
, vol.130
, pp. 413-436
-
-
Matthew, J.B.1
Gurd, F.R.N.2
-
30
-
-
0035370422
-
Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations
-
Nielsen JE, Vriend G. Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations. Proteins 2001;43:403-412.
-
(2001)
Proteins
, vol.43
, pp. 403-412
-
-
Nielsen, J.E.1
Vriend, G.2
-
31
-
-
0035451052
-
What are the dielectric "constants" of proteins and how to validate electrostatic models?
-
Schutz CN, Warshel A. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 2001; 44:400-417.
-
(2001)
Proteins
, vol.44
, pp. 400-417
-
-
Schutz, C.N.1
Warshel, A.2
-
32
-
-
0037474539
-
Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI = 3.5) and a basic variant (pI = 10.2)
-
Laurents DV, Huyghues-Despointes BMP, Bruix M, Thurlkill RL, Schell D, Newsom S, Grimsley GR, Shaw KL, Trevino S, Rico M, Briggs JM, Antesiewicz JM, Scholtz JM, Pace CN. Charge-charge interactions are key determinants of the pK values of ionizable groups in ribonuclease Sa (pI = 3.5) and a basic variant (pI = 10.2). J Mol Biol 2003;325:1077-1092.
-
(2003)
J Mol Biol
, vol.325
, pp. 1077-1092
-
-
Laurents, D.V.1
Huyghues-Despointes, B.M.P.2
Bruix, M.3
Thurlkill, R.L.4
Schell, D.5
Newsom, S.6
Grimsley, G.R.7
Shaw, K.L.8
Trevino, S.9
Rico, M.10
Briggs, J.M.11
Antesiewicz, J.M.12
Scholtz, J.M.13
Pace, C.N.14
-
33
-
-
0037305552
-
On the evaluation and optimization of protein X-ray structures for pKa calculations
-
Nielsen JE, McCammon JA. On the evaluation and optimization of protein X-ray structures for pKa calculations. Protein Sci 2003;12:313-326.
-
(2003)
Protein Sci
, vol.12
, pp. 313-326
-
-
Nielsen, J.E.1
McCammon, J.A.2
-
34
-
-
0036787760
-
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins
-
Georgescu RE, Alexov EG, Gunner MR. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins. Biophys J 2002;83:1731-1748.
-
(2002)
Biophys J
, vol.83
, pp. 1731-1748
-
-
Georgescu, R.E.1
Alexov, E.G.2
Gunner, M.R.3
-
35
-
-
0035960203
-
Conformational averaging in pK calculations: Improvement and limitations in prediction of ionization properties of proteins
-
Koumanov A, Karshikoff A, Friis EP, Borchert TV. Conformational averaging in pK calculations: improvement and limitations in prediction of ionization properties of proteins. J Phys Chem B 2001;105:9339-9344.
-
(2001)
J Phys Chem B
, vol.105
, pp. 9339-9344
-
-
Koumanov, A.1
Karshikoff, A.2
Friis, E.P.3
Borchert, T.V.4
-
36
-
-
0031670370
-
Improving the accuracy of protein pK(a) calculations: Conformational averaging versus the average structure
-
van Vlijmen HWT, Schaefer M, Karplus M. Improving the accuracy of protein pK(a) calculations: conformational averaging versus the average structure. Proteins 1998;33:145-158.
-
(1998)
Proteins
, vol.33
, pp. 145-158
-
-
Van Vlijmen, H.W.T.1
Schaefer, M.2
Karplus, M.3
-
37
-
-
0031564641
-
Modeling of protein conformational fluctuations in pK(a) predictions
-
Zhou HX, Vijayakumar M. Modeling of protein conformational fluctuations in pK(a) predictions. J Mol Biol 1997;267:1002-1011.
-
(1997)
J Mol Biol
, vol.267
, pp. 1002-1011
-
-
Zhou, H.X.1
Vijayakumar, M.2
-
38
-
-
0028859420
-
Conformation and hydrogen ion titration of proteins: A continuum electrostatic model with conformational flexibility
-
You TJ, Bashford D. Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility. Biophys J 1995;69:1721-1733.
-
(1995)
Biophys J
, vol.69
, pp. 1721-1733
-
-
You, T.J.1
Bashford, D.2
-
39
-
-
0033613164
-
Tanford-Kirkwood electrostatics for protein modeling
-
Havranek JJ, Harbury PB. Tanford-Kirkwood electrostatics for protein modeling. Proc Natl Acad Sci USA 1999;96:11145-11150.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 11145-11150
-
-
Havranek, J.J.1
Harbury, P.B.2
-
40
-
-
0028951968
-
Ph, ionic-strength, and temperature dependences of ionization equilibria for the carboxyl groups in turkey ovomucoid 3rd domain
-
Schaller W, Robertson AD. Ph, ionic-strength, and temperature dependences of ionization equilibria for the carboxyl groups in turkey ovomucoid 3rd domain. Biochemistry 1995;34:4714-4723.
-
(1995)
Biochemistry
, vol.34
, pp. 4714-4723
-
-
Schaller, W.1
Robertson, A.D.2
-
41
-
-
0037452862
-
NMR determination of pK(a) values for Asp, Glu, His, and Lys mutants at each variable contiguous enzyme-inhibitor contact position of the turkey ovomucoid third domain
-
Song JK, Laskowski M, Qasim MA, Markley JL. NMR determination of pK(a) values for Asp, Glu, His, and Lys mutants at each variable contiguous enzyme-inhibitor contact position of the turkey ovomucoid third domain. Biochemistry 2003;42:2847-2856.
-
(2003)
Biochemistry
, vol.42
, pp. 2847-2856
-
-
Song, J.K.1
Laskowski, M.2
Qasim, M.A.3
Markley, J.L.4
-
42
-
-
0028904906
-
Hydrogen-bonds and the pH-dependence of ovomucoid 3rd domain stability
-
Swintkruse L, Robertson AD. Hydrogen-bonds and the pH-dependence of ovomucoid 3rd domain stability. Biochemistry 1995;34:4724-4732.
-
(1995)
Biochemistry
, vol.34
, pp. 4724-4732
-
-
Swintkruse, L.1
Robertson, A.D.2
-
43
-
-
0032537485
-
Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain
-
Forsyth WR, Gilson MK, Antosiewicz J, Jaren OR, Robertson AD. Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain. Biochemistry 1998;37:8643-8652.
-
(1998)
Biochemistry
, vol.37
, pp. 8643-8652
-
-
Forsyth, W.R.1
Gilson, M.K.2
Antosiewicz, J.3
Jaren, O.R.4
Robertson, A.D.5
-
44
-
-
84961973524
-
The prediction of protein pK(a)'s using QM/MM: The pK(a) of lysine 55 in turkey ovomucoid third domain
-
Li H, Hains AW, Everts JE, Robertson AD, Jensen JH. The prediction of protein pK(a)'s using QM/MM: the pK(a) of lysine 55 in turkey ovomucoid third domain. J Phys Chem B 2002;106:3486-3494.
-
(2002)
J Phys Chem B
, vol.106
, pp. 3486-3494
-
-
Li, H.1
Hains, A.W.2
Everts, J.E.3
Robertson, A.D.4
Jensen, J.H.5
-
45
-
-
33751500123
-
Absolute Pka calculations with continuum dielectric methods
-
Lim C, Bashford D, Karplus M. Absolute Pka calculations with continuum dielectric methods. J Phys Chem 1991;95:5610-5620.
-
(1991)
J Phys Chem
, vol.95
, pp. 5610-5620
-
-
Lim, C.1
Bashford, D.2
Karplus, M.3
-
46
-
-
33751159055
-
Incorporating solvation effects into density-functional electronic-structure calculations
-
Chen JL, Noodleman L, Case DA, Bashford D. Incorporating solvation effects into density-functional electronic-structure calculations. J Phys Chem 1994;98:11059-11068.
-
(1994)
J Phys Chem
, vol.98
, pp. 11059-11068
-
-
Chen, J.L.1
Noodleman, L.2
Case, D.A.3
Bashford, D.4
-
47
-
-
84962440579
-
Incorporating solvation effects into density functional theory: Calculation of absolute acidities
-
Richardson WH, Peng C, Bashford D, Noodleman L, Case DA. Incorporating solvation effects into density functional theory: calculation of absolute acidities. Int J Quantum Chem 1997;61:207-217.
-
(1997)
Int J Quantum Chem
, vol.61
, pp. 207-217
-
-
Richardson, W.H.1
Peng, C.2
Bashford, D.3
Noodleman, L.4
Case, D.A.5
-
48
-
-
0001591264
-
Calculation of substituent effects on pK(a) values for pyrone and dihydropyrone inhibitors of HIV-1 protease
-
Topol IA, Burt SK, Rashin AA, Erickson JW. Calculation of substituent effects on pK(a) values for pyrone and dihydropyrone inhibitors of HIV-1 protease. J Phys Chem A 2000;104:866-872.
-
(2000)
J Phys Chem A
, vol.104
, pp. 866-872
-
-
Topol, I.A.1
Burt, S.K.2
Rashin, A.A.3
Erickson, J.W.4
-
49
-
-
0035892148
-
Interactions of azodicarbonamide (ADA) species with the model zinc finger site: Theoretical support of the zinc finger domain destruction in the HIV-1 nucleocapsid protein (NCp7) by ADA
-
Topol IA, Nemukhin AV, Dobrogorskaya YI, Burt SK. Interactions of azodicarbonamide (ADA) species with the model zinc finger site: theoretical support of the zinc finger domain destruction in the HIV-1 nucleocapsid protein (NCp7) by ADA. J Phys Chem B 2001;105:11341-11350.
-
(2001)
J Phys Chem B
, vol.105
, pp. 11341-11350
-
-
Topol, I.A.1
Nemukhin, A.V.2
Dobrogorskaya, Y.I.3
Burt, S.K.4
-
50
-
-
0031358013
-
Calculation of absolute and relative acidities of substituted imidazoles in aqueous solvent
-
Topol IA, Tawa GJ, Burt SK, Rashin AA. Calculation of absolute and relative acidities of substituted imidazoles in aqueous solvent. J Phys Chem A 1997;101:10075-10081.
-
(1997)
J Phys Chem A
, vol.101
, pp. 10075-10081
-
-
Topol, I.A.1
Tawa, G.J.2
Burt, S.K.3
Rashin, A.A.4
-
51
-
-
0034287468
-
Acidity of organic molecules in the gas phase and in aqueous solvent
-
Topol IA, Tawa GJ, Caldwell RA, Eissenstat MA, Burt SK. Acidity of organic molecules in the gas phase and in aqueous solvent. J Phys Chem A 2000;104:9619-9624.
-
(2000)
J Phys Chem A
, vol.104
, pp. 9619-9624
-
-
Topol, I.A.1
Tawa, G.J.2
Caldwell, R.A.3
Eissenstat, M.A.4
Burt, S.K.5
-
52
-
-
0035127984
-
First principles calculation of pK(a) values for 5-substituted uracils
-
Jang YH, Sowers LC, Cagin T, Goddard WA. First principles calculation of pK(a) values for 5-substituted uracils. J Phys Chem A 2001;105:274-280.
-
(2001)
J Phys Chem A
, vol.105
, pp. 274-280
-
-
Jang, Y.H.1
Sowers, L.C.2
Cagin, T.3
Goddard, W.A.4
-
53
-
-
84961981283
-
Prediction of the pK(a) of carboxylic acids using the ab initio continuum-solvation model PCM-UAHF
-
Schuurmann G, Cossi M, Barone V, Tomasi J. Prediction of the pK(a) of carboxylic acids using the ab initio continuum-solvation model PCM-UAHF. J Phys Chem A 1998;102:6706-6712.
-
(1998)
J Phys Chem A
, vol.102
, pp. 6706-6712
-
-
Schuurmann, G.1
Cossi, M.2
Barone, V.3
Tomasi, J.4
-
54
-
-
28944439105
-
Ab initio calculations of absolute pK(a) values in aqueous solution I. Carboxylic acids
-
da Silva CO, da Silva EC, Nascimento MAC. Ab initio calculations of absolute pK(a) values in aqueous solution I. Carboxylic acids. J Phys Chem A 1999;103:11194-11199.
-
(1999)
J Phys Chem A
, vol.103
, pp. 11194-11199
-
-
Da Silva, C.O.1
Da Silva, E.C.2
Nascimento, M.A.C.3
-
55
-
-
0034704774
-
Ab initio calculations of absolute pK(a) values in aqueous solution. II. Aliphatic alcohols, thiols, and halogenated carboxylic acids
-
Silva CO, da Silva EC, Nascimento MAC. Ab initio calculations of absolute pK(a) values in aqueous solution. II. Aliphatic alcohols, thiols, and halogenated carboxylic acids. J Phys Chem A 2000;104: 2402-2409.
-
(2000)
J Phys Chem A
, vol.104
, pp. 2402-2409
-
-
Silva, C.O.1
Da Silva, E.C.2
Nascimento, M.A.C.3
-
56
-
-
84961974409
-
Absolute pK(a) determinations for substituted phenols
-
Liptak MD, Gross KC, Seybold PG, Feldgus S, Shields GC. Absolute pK(a) determinations for substituted phenols. J Am Chem Soc 2002;124:6421-6427.
-
(2002)
J Am Chem Soc
, vol.124
, pp. 6421-6427
-
-
Liptak, M.D.1
Gross, K.C.2
Seybold, P.G.3
Feldgus, S.4
Shields, G.C.5
-
57
-
-
84962424896
-
Experimentation with different thermodynamic cycles used for pK(a) calculations on carboxylic acids using complete basis set and gaussian-n models combined with CPCM continuum solvation methods
-
Liptak MD, Shields GC. Experimentation with different thermodynamic cycles used for pK(a) calculations on carboxylic acids using complete basis set and gaussian-n models combined with CPCM continuum solvation methods. Int J Quantum Chem 2001;85:727-741.
-
(2001)
Int J Quantum Chem
, vol.85
, pp. 727-741
-
-
Liptak, M.D.1
Shields, G.C.2
-
58
-
-
84962359443
-
Accurate pK(a) calculations for carboxylic acids using complete basis set and gaussian-n models combined with CPCM continuum solvation methods
-
Liptak MD, Shields GC. Accurate pK(a) calculations for carboxylic acids using complete basis set and gaussian-n models combined with CPCM continuum solvation methods. J Am Chem Soc 2001;123:7314-7319.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 7314-7319
-
-
Liptak, M.D.1
Shields, G.C.2
-
59
-
-
0037104738
-
Computation of pK(a) from dielectric continuum theory
-
Chipman DM. Computation of pK(a) from dielectric continuum theory. J Phys Chem A 2002;106:7413-7422.
-
(2002)
J Phys Chem A
, vol.106
, pp. 7413-7422
-
-
Chipman, D.M.1
-
60
-
-
0037149134
-
Accurate prediction of acidity constants in aqueous solution via density functional theory and self-consistent reaction field methods
-
Klicic JJ, Friesner RA, Liu SY, Guida WC. Accurate prediction of acidity constants in aqueous solution via density functional theory and self-consistent reaction field methods. J Phys Chem A 2002; 106:1327-1335.
-
(2002)
J Phys Chem A
, vol.106
, pp. 1327-1335
-
-
Klicic, J.J.1
Friesner, R.A.2
Liu, S.Y.3
Guida, W.C.4
-
61
-
-
0037165455
-
Theoretical determination of two structural forms of the active site in cadmium-containing phosphotriesterases
-
Zheng F, Zhan CG, Ornstein RL. Theoretical determination of two structural forms of the active site in cadmium-containing phosphotriesterases. J Phys Chem B 2002;106:717-722.
-
(2002)
J Phys Chem B
, vol.106
, pp. 717-722
-
-
Zheng, F.1
Zhan, C.G.2
Ornstein, R.L.3
-
62
-
-
2442509416
-
Computing macroscopic and microscopic pK(a) vaules of the Rieske iron-sulfur cluster using a combined electrostatic-density functional method
-
Ullmann GM, Noodleman L, Case DA. Computing macroscopic and microscopic pK(a) vaules of the Rieske iron-sulfur cluster using a combined electrostatic-density functional method. J Inorg Biochem 2001;86:464.
-
(2001)
J Inorg Biochem
, vol.86
, pp. 464
-
-
Ullmann, G.M.1
Noodleman, L.2
Case, D.A.3
-
63
-
-
0036933444
-
Density functional calculation of pK(a) values and redox potentials in the bovine Rieske iron-sulfur protein
-
Ullmann GM, Noodleman L, Case DA. Density functional calculation of pK(a) values and redox potentials in the bovine Rieske iron-sulfur protein. J Biol Inorg Chem 2002;7:632-639.
-
(2002)
J Biol Inorg Chem
, vol.7
, pp. 632-639
-
-
Ullmann, G.M.1
Noodleman, L.2
Case, D.A.3
-
65
-
-
84893169025
-
General atomic and molecular electronic structure system
-
Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, et al. General atomic and molecular electronic structure system. J Comput Chem 1993;14:1347-1363.
-
(1993)
J Comput Chem
, vol.14
, pp. 1347-1363
-
-
Schmidt, M.W.1
Baldridge, K.K.2
Boatz, J.A.3
Elbert, S.T.4
Gordon, M.S.5
Jensen, J.H.6
Koseki, S.7
Matsunaga, N.8
Nguyen, K.A.9
-
66
-
-
2442595497
-
-
Fayetteville, AR; sales@pqs-chem.com. z.pqs-chem.com; sales@pqs-chem.com
-
PQS version 2.4 PQS, Fayetteville, AR, http://www.pqs-chem.com; sales@pqs-chem.com. z.pqs-chem.com; sales@pqs-chem.com.
-
PQS Version 2.4 PQS
-
-
-
67
-
-
0031209054
-
A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics
-
Cances E, Mennucci B, Tomasi J. A new integral equation formalism for the polarizable continuum model: theoretical background and applications to isotropic and anisotropic dielectrics. J Chem Phys 1997;107:3032-3041.
-
(1997)
J Chem Phys
, vol.107
, pp. 3032-3041
-
-
Cances, E.1
Mennucci, B.2
Tomasi, J.3
-
68
-
-
0022801412
-
X-ray crystal-structure of the complex of human-leukocyte elastase (Pmn Elastase) and the 3rd domain of the turkey ovomucoid inhibitor
-
Bode W, Wei AZ, Huber R, Meyer E, Travis J, Neumann S. X-ray crystal-structure of the complex of human-leukocyte elastase (Pmn Elastase) and the 3rd domain of the turkey ovomucoid inhibitor. EMBO J 1986;5:2453-2458.
-
(1986)
EMBO J
, vol.5
, pp. 2453-2458
-
-
Bode, W.1
Wei, A.Z.2
Huber, R.3
Meyer, E.4
Travis, J.5
Neumann, S.6
-
69
-
-
0030442990
-
Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
-
Hooft RWW, Sander C, Vriend G. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins 1996;26:363-376.
-
(1996)
Proteins
, vol.26
, pp. 363-376
-
-
Hooft, R.W.W.1
Sander, C.2
Vriend, G.3
-
70
-
-
84962450193
-
-
http://www.cmbi.kun.nl/gv/servers/WIWWWI/.
-
-
-
-
72
-
-
0001461682
-
Examination of titration behavior
-
Nozaki Y, Tanford C. Examination of titration behavior. Methods Enzymol 1967;11:715-734.
-
(1967)
Methods Enzymol
, vol.11
, pp. 715-734
-
-
Nozaki, Y.1
Tanford, C.2
-
73
-
-
0034091669
-
Backbone dipoles generate positive potentials in all proteins: Origins and implications of the effect
-
Gunner MR, Saleh MA, Cross E, ud-Doula A, Wise M. Backbone dipoles generate positive potentials in all proteins: origins and implications of the effect. Biophys J 2000;78:1126-1144.
-
(2000)
Biophys J
, vol.78
, pp. 1126-1144
-
-
Gunner, M.R.1
Saleh, M.A.2
Cross, E.3
Ud-Doula, A.4
Wise, M.5
-
75
-
-
0034062925
-
Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures
-
Eswar N, Ramakrishnan C. Deterministic features of side-chain main-chain hydrogen bonds in globular protein structures. Protein Eng 2000;13:227-238.
-
(2000)
Protein Eng
, vol.13
, pp. 227-238
-
-
Eswar, N.1
Ramakrishnan, C.2
-
76
-
-
0035964164
-
Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase
-
Joshi MD, Sidhu G, Nielsen JE, Brayer GD, Withers SG, McIntosh LP. Dissecting the electrostatic interactions and pH-dependent activity of a family 11 glycosidase. Biochemistry 2001;40:10115-10139.
-
(2001)
Biochemistry
, vol.40
, pp. 10115-10139
-
-
Joshi, M.D.1
Sidhu, G.2
Nielsen, J.E.3
Brayer, G.D.4
Withers, S.G.5
McIntosh, L.P.6
-
77
-
-
0035797915
-
An unusually low pK(a) for Cys282 in the active site of human muscle creatine kinase
-
Wang PF, McLeish MJ, Kneen MM, Lee G, Kenyon GL. An unusually low pK(a) for Cys282 in the active site of human muscle creatine kinase. Biochemistry 2001;40:11698-11705.
-
(2001)
Biochemistry
, vol.40
, pp. 11698-11705
-
-
Wang, P.F.1
McLeish, M.J.2
Kneen, M.M.3
Lee, G.4
Kenyon, G.L.5
-
78
-
-
0030612614
-
Use of H-1 NMR spectroscopy and computer simulations to analyze histidine pK(a) changes in a protein tyrosine phosphatase: Experimental and theoretical determination of electrostatic properties in a small protein
-
Tishmack PA, Bashford D, Harms E, VanEtten RL. Use of H-1 NMR spectroscopy and computer simulations to analyze histidine pK(a) changes in a protein tyrosine phosphatase: experimental and theoretical determination of electrostatic properties in a small protein. Biochemistry 1997;36:11984-11994.
-
(1997)
Biochemistry
, vol.36
, pp. 11984-11994
-
-
Tishmack, P.A.1
Bashford, D.2
Harms, E.3
VanEtten, R.L.4
-
79
-
-
0036228118
-
Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein
-
Lee KK, Fitch CA, Garcia-Moreno B. Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein. Protein Sci 2002;11:1004-1016.
-
(2002)
Protein Sci
, vol.11
, pp. 1004-1016
-
-
Lee, K.K.1
Fitch, C.A.2
Garcia-Moreno, B.3
-
80
-
-
0029666454
-
The pK(a) of the general acid/base carboxyl group of a glycosidase cycles during catalysis: A C-13-NMR study of Bacillus circuluns xylanase
-
McIntosh LP, Hand G, Johnson PE, Joshi MD, Korner M, Plesniak LA, Ziser L, Wakarchuk WW, Withers SG. The pK(a) of the general acid/base carboxyl group of a glycosidase cycles during catalysis: a C-13-NMR study of Bacillus circuluns xylanase. Biochemistry 1996;35:9958-9966.
-
(1996)
Biochemistry
, vol.35
, pp. 9958-9966
-
-
McIntosh, L.P.1
Hand, G.2
Johnson, P.E.3
Joshi, M.D.4
Korner, M.5
Plesniak, L.A.6
Ziser, L.7
Wakarchuk, W.W.8
Withers, S.G.9
-
81
-
-
0032535188
-
Coulombic effects of remote subsites on the active site of ribonuclease A
-
Fisher BM, Schultz LW, Raines RT. Coulombic effects of remote subsites on the active site of ribonuclease A. Biochemistry 1998;37: 17386-17401.
-
(1998)
Biochemistry
, vol.37
, pp. 17386-17401
-
-
Fisher, B.M.1
Schultz, L.W.2
Raines, R.T.3
-
82
-
-
0037379163
-
Anion binding to a protein-protein complex lacks dependence on net charge
-
Waldron TT, Modestou MA, Murphy KP. Anion binding to a protein-protein complex lacks dependence on net charge. Protein Sci 2003;12:871-874.
-
(2003)
Protein Sci
, vol.12
, pp. 871-874
-
-
Waldron, T.T.1
Modestou, M.A.2
Murphy, K.P.3
-
83
-
-
0036890275
-
Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations
-
Ren PY, Ponder JW. Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J Comput Chem 2002;23:1497-1506.
-
(2002)
J Comput Chem
, vol.23
, pp. 1497-1506
-
-
Ren, P.Y.1
Ponder, J.W.2
-
84
-
-
0036882094
-
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests
-
Kaminski GA, Stern HA, Berne BJ, Friesner RA, Cao YXX, Murphy RB, Zhou RH, Halgren TA. Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. J Comput Chem 2002;23: 1515-1531.
-
(2002)
J Comput Chem
, vol.23
, pp. 1515-1531
-
-
Kaminski, G.A.1
Stern, H.A.2
Berne, B.J.3
Friesner, R.A.4
Cao, Y.X.X.5
Murphy, R.B.6
Zhou, R.H.7
Halgren, T.A.8
-
86
-
-
84961981991
-
A new definition of cavities for the computation of solvation free energies by the polarizable continuum model
-
Barone V, Cossi M, Tomasi J. A new definition of cavities for the computation of solvation free energies by the polarizable continuum model. J Chem Phys 1997;107:3210-3221.
-
(1997)
J Chem Phys
, vol.107
, pp. 3210-3221
-
-
Barone, V.1
Cossi, M.2
Tomasi, J.3
-
87
-
-
84946893847
-
Electrostatic interaction of a solute with a continuum - A direct utilization of ab initio molecular potentials for the prevision of solvent effects
-
Miertus S, Scrocco E, Tomasi J. Electrostatic interaction of a solute with a continuum - a direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chem Phys 1981;55:117-129.
-
(1981)
Chem Phys
, vol.55
, pp. 117-129
-
-
Miertus, S.1
Scrocco, E.2
Tomasi, J.3
-
88
-
-
33747754400
-
A scaled particle theory of aqueous and nonaqueous solutions
-
Pierotti RA. A scaled particle theory of aqueous and nonaqueous solutions. Chem Rev 1979;76:717-726.
-
(1979)
Chem Rev
, vol.76
, pp. 717-726
-
-
Pierotti, R.A.1
-
89
-
-
84986533294
-
Dispersion and repulsion contributions to the solvation energy-refinements to a simple computational model in the continuum approximation
-
Floris FM, Tomasi J, Ahuir JLP. Dispersion and repulsion contributions to the solvation energy-refinements to a simple computational model in the continuum approximation. J Comput Chem 1991;12:784-791.
-
(1991)
J Comput Chem
, vol.12
, pp. 784-791
-
-
Floris, F.M.1
Tomasi, J.2
Ahuir, J.L.P.3
-
90
-
-
84962440509
-
Reaction field effects on nitrogen shielding
-
Zhan CG, Chipman DM. Reaction field effects on nitrogen shielding. J Chem Phys 1999;110:1611-1622.
-
(1999)
J Chem Phys
, vol.110
, pp. 1611-1622
-
-
Zhan, C.G.1
Chipman, D.M.2
|