-
1
-
-
0030945495
-
Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties
-
Alexov E.G., and Gunner M.R. Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties. Biophys. J. 72 (1997) 2075-2093
-
(1997)
Biophys. J.
, vol.72
, pp. 2075-2093
-
-
Alexov, E.G.1
Gunner, M.R.2
-
2
-
-
0033614791
-
Calculated protein and proton motions coupled to electron transfer: Electron transfer from QA- to QB in bacterial photosynthetic reaction centers
-
Alexov E.G., and Gunner M.R. Calculated protein and proton motions coupled to electron transfer: Electron transfer from QA- to QB in bacterial photosynthetic reaction centers. Biochemistry 38 (1999) 8253-8270
-
(1999)
Biochemistry
, vol.38
, pp. 8253-8270
-
-
Alexov, E.G.1
Gunner, M.R.2
-
3
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker N.A., Sept D., Joseph S., Holst M.J., and McCammon J.A. Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98 (2001) 10037-10041
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
4
-
-
34447297323
-
Energetics of protein folding
-
Baldwin R.L. Energetics of protein folding. J. Mol. Biol. 371 (2007) 283-301
-
(2007)
J. Mol. Biol.
, vol.371
, pp. 283-301
-
-
Baldwin, R.L.1
-
5
-
-
0036732086
-
Constant-pH molecular dynamics using stochastic titration
-
Baptista A.M., Teixeira V.H., and Soares C.M. Constant-pH molecular dynamics using stochastic titration. J. Chem. Phys. 117 (2002) 4184-4200
-
(2002)
J. Chem. Phys.
, vol.117
, pp. 4184-4200
-
-
Baptista, A.M.1
Teixeira, V.H.2
Soares, C.M.3
-
6
-
-
0026095641
-
Protonation of interacting residues in a protein by a Monte Carlo method: Application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides
-
Beroza P., Fredkin D.R., Okamura M.Y., and Feher G. Protonation of interacting residues in a protein by a Monte Carlo method: Application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides. Proc. Natl. Acad. Sci. USA 88 (1991) 5804-5808
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.88
, pp. 5804-5808
-
-
Beroza, P.1
Fredkin, D.R.2
Okamura, M.Y.3
Feher, G.4
-
7
-
-
41649119572
-
Pore-opening mechanism of the nicotinic acetylcholine receptor evinced by proton transfer
-
Cymes G.D., and Grosman C. Pore-opening mechanism of the nicotinic acetylcholine receptor evinced by proton transfer. Nat. Struct. Mol. Biol. 15 (2008) 389-396
-
(2008)
Nat. Struct. Mol. Biol.
, vol.15
, pp. 389-396
-
-
Cymes, G.D.1
Grosman, C.2
-
8
-
-
33748593093
-
Improving the continuum dielectric approach to calculating pKas of ionizable groups in proteins
-
Demchuk E., and Wade R.C. Improving the continuum dielectric approach to calculating pKas of ionizable groups in proteins. J. Phys. Chem. 100 (1996) 17373-17387
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 17373-17387
-
-
Demchuk, E.1
Wade, R.C.2
-
9
-
-
34547559704
-
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
-
Dolinsky T.J., Czodrowski P., Li H., Nielsen J.E., Jensen J.H., Klebe G., and Baker N.A. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35 (2007) W522-W525
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Dolinsky, T.J.1
Czodrowski, P.2
Li, H.3
Nielsen, J.E.4
Jensen, J.H.5
Klebe, G.6
Baker, N.A.7
-
10
-
-
3242886771
-
PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
-
Dolinsky T.J., Nielsen J.E., McCammon J.A., and Baker N.A. PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 32 (2004) W665-W667
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Dolinsky, T.J.1
Nielsen, J.E.2
McCammon, J.A.3
Baker, N.A.4
-
11
-
-
0035965145
-
Prediction of functionally important residues based solely on the computed energetics of protein structure
-
Elcock A.H. Prediction of functionally important residues based solely on the computed energetics of protein structure. J. Mol. Biol. 312 (2001) 885-896
-
(2001)
J. Mol. Biol.
, vol.312
, pp. 885-896
-
-
Elcock, A.H.1
-
12
-
-
0036787760
-
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins
-
Georgescu R.E., Alexov E.G., and Gunner M.R. Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins. Biophys. J. 83 (2002) 1731-1748
-
(2002)
Biophys. J.
, vol.83
, pp. 1731-1748
-
-
Georgescu, R.E.1
Alexov, E.G.2
Gunner, M.R.3
-
13
-
-
23144457576
-
H++: A server for estimating pKas and adding missing hydrogens to macromolecules
-
Gordon J.C., Myers J.B., Folta T., Shoja V., Heath L.S., and Onufriev A. H++: A server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res. 33 (2005) W368-W371
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Gordon, J.C.1
Myers, J.B.2
Folta, T.3
Shoja, V.4
Heath, L.S.5
Onufriev, A.6
-
14
-
-
0034716940
-
Hydrogen bonding and catalysis: A novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase
-
Joshi M.D., Sidhu G., Pot I., Brayer G.D., Withers S.G., and McIntosh L.P. Hydrogen bonding and catalysis: A novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase. J. Mol. Biol. 299 (2000) 255-279
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 255-279
-
-
Joshi, M.D.1
Sidhu, G.2
Pot, I.3
Brayer, G.D.4
Withers, S.G.5
McIntosh, L.P.6
-
15
-
-
23244440384
-
Constant pH molecular dynamics with proton tautomerism
-
Khandogin J., and Brooks III C.L. Constant pH molecular dynamics with proton tautomerism. Biophys. J. 89 (2005) 141-157
-
(2005)
Biophys. J.
, vol.89
, pp. 141-157
-
-
Khandogin, J.1
Brooks III, C.L.2
-
16
-
-
28644432877
-
Very fast empirical prediction and rationalization of protein pKa values
-
Li H., Robertson A.D., and Jensen J.H. Very fast empirical prediction and rationalization of protein pKa values. Proteins 61 (2005) 704-721
-
(2005)
Proteins
, vol.61
, pp. 704-721
-
-
Li, H.1
Robertson, A.D.2
Jensen, J.H.3
-
18
-
-
0029633152
-
Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian Dynamics Program
-
Madura J.D., Briggs J.M., Wade R.C., Davis M.E., Luty B.A., Ilin A., Antosiewicz J., Gilso M.K., Bagheri B., Scott L.R., and McCammon J.A. Electrostatics and diffusion of molecules in solution: Simulations with the University of Houston Brownian Dynamics Program. Comput. Phys. Commun. 91 (1995) 57-95
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 57-95
-
-
Madura, J.D.1
Briggs, J.M.2
Wade, R.C.3
Davis, M.E.4
Luty, B.A.5
Ilin, A.6
Antosiewicz, J.7
Gilso, M.K.8
Bagheri, B.9
Scott, L.R.10
McCammon, J.A.11
-
19
-
-
0029666454
-
The pKa of the general acid/base carboxyl group of a glycosidase cycles during catalysis: A 13C-NMR study of Bacillus circulans xylanase
-
McIntosh L.P., Hand G., Johnson P.E., Joshi M.D., Körner M., Plesniak L.A., Ziser L., Wakarchuk W.W., and Withers S.G. The pKa of the general acid/base carboxyl group of a glycosidase cycles during catalysis: A 13C-NMR study of Bacillus circulans xylanase. Biochemistry 35 (1996) 9958-9966
-
(1996)
Biochemistry
, vol.35
, pp. 9958-9966
-
-
McIntosh, L.P.1
Hand, G.2
Johnson, P.E.3
Joshi, M.D.4
Körner, M.5
Plesniak, L.A.6
Ziser, L.7
Wakarchuk, W.W.8
Withers, S.G.9
-
20
-
-
9244223045
-
Constant pH molecular dynamics in generalized Born implicit solvent
-
Mongan J., Case D.A., and McCammon J.A. Constant pH molecular dynamics in generalized Born implicit solvent. J. Comput. Chem. 25 (2004) 2038-2048
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 2038-2048
-
-
Mongan, J.1
Case, D.A.2
McCammon, J.A.3
-
21
-
-
33646794930
-
A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules
-
Myers J., Grothaus G., Narayanan S., and Onufriev A. A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules. Proteins 63 (2006) 928-938
-
(2006)
Proteins
, vol.63
, pp. 928-938
-
-
Myers, J.1
Grothaus, G.2
Narayanan, S.3
Onufriev, A.4
-
22
-
-
84986486656
-
A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
-
Nicholls A., and Honig B. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comp. Chem. 12 (1991) 435-445
-
(1991)
J. Comp. Chem.
, vol.12
, pp. 435-445
-
-
Nicholls, A.1
Honig, B.2
-
23
-
-
33846614924
-
Analysing the pH-dependent properties of proteins using pKa calculations
-
Nielsen J.E. Analysing the pH-dependent properties of proteins using pKa calculations. J. Mol. Graph. 25 (2006) 691-699
-
(2006)
J. Mol. Graph.
, vol.25
, pp. 691-699
-
-
Nielsen, J.E.1
-
24
-
-
59649119370
-
-
University College Dublin, Dublin, Ireland
-
Nielsen J.E. pKaTool (2006), University College Dublin, Dublin, Ireland. http://enzyme.ucd.ie/Science/pKa/pKaTool
-
(2006)
pKaTool
-
-
Nielsen, J.E.1
-
25
-
-
0037305552
-
On the evaluation and optimisation of protein X-ray structures for pKa calculations
-
Nielsen J.E., and McCammon J.A. On the evaluation and optimisation of protein X-ray structures for pKa calculations. Protein Sci. 12 (2003) 313-326
-
(2003)
Protein Sci.
, vol.12
, pp. 313-326
-
-
Nielsen, J.E.1
McCammon, J.A.2
-
26
-
-
0035370422
-
Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations
-
Nielsen J.E., and Vriend G. Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations. Proteins 43 (2001) 403-412
-
(2001)
Proteins
, vol.43
, pp. 403-412
-
-
Nielsen, J.E.1
Vriend, G.2
-
27
-
-
0035940421
-
THEMATICS: A simple computational predictor of enzyme function from structure
-
Ondrechen M.J., Clifton J.G., and Ringe D. THEMATICS: A simple computational predictor of enzyme function from structure. Proc. Natl. Acad. Sci. USA 98 (2001) 12473-12478
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 12473-12478
-
-
Ondrechen, M.J.1
Clifton, J.G.2
Ringe, D.3
-
28
-
-
45549107077
-
Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase
-
Pisliakov A.V., Sharma P.K., Chu Z.T., Haranczyk M., and Warshel A. Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase. Proc. Natl. Acad. Sci. USA 105 (2008) 7726-7731
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 7726-7731
-
-
Pisliakov, A.V.1
Sharma, P.K.2
Chu, Z.T.3
Haranczyk, M.4
Warshel, A.5
-
29
-
-
0010624785
-
The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins
-
Sham Y.Y., Muegge I., and Warshel A. The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins. Biophys. J. 74 (1998) 1744-1753
-
(1998)
Biophys. J.
, vol.74
, pp. 1744-1753
-
-
Sham, Y.Y.1
Muegge, I.2
Warshel, A.3
-
30
-
-
38048998514
-
Determination of electrostatic interaction energies and protonation state populations in enzyme active sites by global fits of NMR-titration data and pH-activity profiles
-
Søndergaard C.R., McIntosh L.P., Pollastri G., and Nielsen J.E. Determination of electrostatic interaction energies and protonation state populations in enzyme active sites by global fits of NMR-titration data and pH-activity profiles. J. Mol. Biol. 376 (2008) 269-287
-
(2008)
J. Mol. Biol.
, vol.376
, pp. 269-287
-
-
Søndergaard, C.R.1
McIntosh, L.P.2
Pollastri, G.3
Nielsen, J.E.4
-
31
-
-
33644697915
-
Protein stability and surface electrostatics: A charged relationship
-
Strickler S.S., Gribenko A.V., Gribenko A.V., Keiffer T.R., Tomlinson J., Reihle T., Loladze V.V., and Makhatadze G.I. Protein stability and surface electrostatics: A charged relationship. Biochemistry 45 (2006) 2761-2766
-
(2006)
Biochemistry
, vol.45
, pp. 2761-2766
-
-
Strickler, S.S.1
Gribenko, A.V.2
Gribenko, A.V.3
Keiffer, T.R.4
Tomlinson, J.5
Reihle, T.6
Loladze, V.V.7
Makhatadze, G.I.8
-
32
-
-
0014718113
-
Protein denaturation. Part C. Theoretical models for the mechanism of denaturation
-
Tanford C. Protein denaturation. Part C. Theoretical models for the mechanism of denaturation. Adv. Protein Chem. 25 (1970) 1-95
-
(1970)
Adv. Protein Chem.
, vol.25
, pp. 1-95
-
-
Tanford, C.1
-
33
-
-
0015520587
-
Interpretation of protein titration curves: Application to lysozyme
-
Tanford C., and Roxby R. Interpretation of protein titration curves: Application to lysozyme. Biochemistry 11 (1972) 2193-2198
-
(1972)
Biochemistry
, vol.11
, pp. 2193-2198
-
-
Tanford, C.1
Roxby, R.2
-
34
-
-
33644876024
-
PPD v1.0-an integrated, web-accessible database of experimentally determined protein pKa values
-
Toseland C.P., McSparron H., Davies M.N., and Flower D.R. PPD v1.0-an integrated, web-accessible database of experimentally determined protein pKa values. Nucleic Acids Res. 34 (2006) D199-D203
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Toseland, C.P.1
McSparron, H.2
Davies, M.N.3
Flower, D.R.4
-
37
-
-
0025398721
-
WHAT IF: A molecular modeling and drug design program
-
29
-
Vriend G. WHAT IF: A molecular modeling and drug design program. J. Mol. Graph 8 (1990) 52-56 29
-
(1990)
J. Mol. Graph
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
39
-
-
0027563464
-
On the calculation of pKas in proteins
-
Yang A.S., Gunner M.R., Sampogna R., Sharp K., and Honig B. On the calculation of pKas in proteins. Proteins 15 (1993) 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
|