-
1
-
-
0030802904
-
Conformational stabilities of Escherichia coli RNase HI variants with a series of amino acid substitutions at a cavity within the hydrophobic core
-
Akasako A, Haruki M, Oobatake M, Kanaya S, (1997) Conformational stabilities of Escherichia coli RNase HI variants with a series of amino acid substitutions at a cavity within the hydrophobic core. J Biol Chem 272: 18686-18693.
-
(1997)
J Biol Chem
, vol.272
, pp. 18686-18693
-
-
Akasako, A.1
Haruki, M.2
Oobatake, M.3
Kanaya, S.4
-
2
-
-
70349336351
-
Increasing protein stability by improving beta-turns
-
Fu H, Grimsley GR, Razvi A, Scholtz JM, Pace CN, (2009) Increasing protein stability by improving beta-turns. Proteins 77: 491-498.
-
(2009)
Proteins
, vol.77
, pp. 491-498
-
-
Fu, H.1
Grimsley, G.R.2
Razvi, A.3
Scholtz, J.M.4
Pace, C.N.5
-
3
-
-
0032872888
-
Increasing protein stability by altering long-range coulombic interactions
-
Grimsley GR, Shaw KL, Fee LR, Alston RW, Huyghues-Despointes BM, et al. (1999) Increasing protein stability by altering long-range coulombic interactions. Protein Sci 8: 1843-1849.
-
(1999)
Protein Sci
, vol.8
, pp. 1843-1849
-
-
Grimsley, G.R.1
Shaw, K.L.2
Fee, L.R.3
Alston, R.W.4
Huyghues-Despointes, B.M.5
-
4
-
-
0033548543
-
Increased helix and protein stability through the introduction of a new tertiary hydrogen bond
-
Peterson RW, Nicholson EM, Thapar R, Klevit RE, Scholtz JM, (1999) Increased helix and protein stability through the introduction of a new tertiary hydrogen bond. J Mol Biol 286: 1609-1619.
-
(1999)
J Mol Biol
, vol.286
, pp. 1609-1619
-
-
Peterson, R.W.1
Nicholson, E.M.2
Thapar, R.3
Klevit, R.E.4
Scholtz, J.M.5
-
5
-
-
0033135227
-
Computational protein design
-
Street AG, Mayo SL, (1999) Computational protein design. Structure 7: R105-109.
-
(1999)
Structure
, vol.7
-
-
Street, A.G.1
Mayo, S.L.2
-
6
-
-
0035782661
-
Protein design-where we were, where we are, where we're going
-
Pokala N, Handel TM, (2001) Protein design-where we were, where we are, where we're going. J Struct Biol 134: 269-281.
-
(2001)
J Struct Biol
, vol.134
, pp. 269-281
-
-
Pokala, N.1
Handel, T.M.2
-
7
-
-
0041387567
-
A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins
-
Dantas G, Kuhlman B, Callender D, Wong M, Baker D, (2003) A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. J Mol Biol 332: 449-460.
-
(2003)
J Mol Biol
, vol.332
, pp. 449-460
-
-
Dantas, G.1
Kuhlman, B.2
Callender, D.3
Wong, M.4
Baker, D.5
-
8
-
-
33749055081
-
Consensus design as a tool for engineering repeat proteins
-
Kajander T, Cortajarena AL, Regan L, (2006) Consensus design as a tool for engineering repeat proteins. Methods Mol Biol 340: 151-170.
-
(2006)
Methods Mol Biol
, vol.340
, pp. 151-170
-
-
Kajander, T.1
Cortajarena, A.L.2
Regan, L.3
-
9
-
-
36448996957
-
Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions
-
Schweiker KL, Zarrine-Afsar A, Davidson AR, Makhatadze GI, (2007) Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions. Protein Sci 16: 2694-2702.
-
(2007)
Protein Sci
, vol.16
, pp. 2694-2702
-
-
Schweiker, K.L.1
Zarrine-Afsar, A.2
Davidson, A.R.3
Makhatadze, G.I.4
-
10
-
-
0033554840
-
Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface
-
Loladze VV, Ibarra-Molero B, Sanchez-Ruiz JM, Makhatadze GI, (1999) Engineering a thermostable protein via optimization of charge-charge interactions on the protein surface. Biochemistry 38: 16419-16423.
-
(1999)
Biochemistry
, vol.38
, pp. 16419-16423
-
-
Loladze, V.V.1
Ibarra-Molero, B.2
Sanchez-Ruiz, J.M.3
Makhatadze, G.I.4
-
12
-
-
59649107985
-
A computational approach for the rational design of stable proteins and enzymes: optimization of surface charge-charge interactions
-
Schweiker KL, Makhatadze GI, (2009) A computational approach for the rational design of stable proteins and enzymes: optimization of surface charge-charge interactions. Methods Enzymol 454: 175-211.
-
(2009)
Methods Enzymol
, vol.454
, pp. 175-211
-
-
Schweiker, K.L.1
Makhatadze, G.I.2
-
13
-
-
62449335519
-
Protein stabilization by the rational design of surface charge-charge interactions
-
Schweiker KL, Makhatadze GI, (2009) Protein stabilization by the rational design of surface charge-charge interactions. Methods Mol Biol 490: 261-283.
-
(2009)
Methods Mol Biol
, vol.490
, pp. 261-283
-
-
Schweiker, K.L.1
Makhatadze, G.I.2
-
14
-
-
62449293337
-
Rational stabilization of enzymes by computational redesign of surface charge-charge interactions
-
Gribenko AV, Patel MM, Liu J, McCallum SA, Wang C, et al. (2009) Rational stabilization of enzymes by computational redesign of surface charge-charge interactions. Proc Natl Acad Sci U S A 106: 2601-2606.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 2601-2606
-
-
Gribenko, A.V.1
Patel, M.M.2
Liu, J.3
McCallum, S.A.4
Wang, C.5
-
15
-
-
33644697915
-
Protein stability and surface electrostatics: a charged relationship
-
Strickler SS, Gribenko AV, Gribenko AV, Keiffer TR, Tomlinson J, et al. (2006) Protein stability and surface electrostatics: a charged relationship. Biochemistry 45: 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
-
16
-
-
0000449960
-
Response: how much solar radiation do clouds absorb?
-
Lumb KJ, Kim PS, (1996) Response: how much solar radiation do clouds absorb? Science 271: 1137-1138.
-
(1996)
Science
, vol.271
, pp. 1137-1138
-
-
Lumb, K.J.1
Kim, P.S.2
-
17
-
-
0026800672
-
Analysis of the heat capacity dependence of protein folding
-
Yang AS, Sharp KA, Honig B, (1992) Analysis of the heat capacity dependence of protein folding. J Mol Biol 227: 889-900.
-
(1992)
J Mol Biol
, vol.227
, pp. 889-900
-
-
Yang, A.S.1
Sharp, K.A.2
Honig, B.3
-
18
-
-
1242299059
-
Protein stabilization by salt bridges: concepts, experimental approaches and clarification of some misunderstandings
-
Bosshard HR, Marti DN, Jelesarov I, (2004) Protein stabilization by salt bridges: concepts, experimental approaches and clarification of some misunderstandings. J Mol Recognit 17: 1-16.
-
(2004)
J Mol Recognit
, vol.17
, pp. 1-16
-
-
Bosshard, H.R.1
Marti, D.N.2
Jelesarov, I.3
-
19
-
-
0033850087
-
High apparent dielectric constants in the interior of a protein reflect water penetration
-
Dwyer JJ, Gittis AG, Karp DA, Lattman EE, Spencer DS, et al. (2000) High apparent dielectric constants in the interior of a protein reflect water penetration. Biophysical Journal 79: 1610-1620.
-
(2000)
Biophysical Journal
, 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
-
20
-
-
0036099192
-
Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration
-
Fitch CA, Karp DA, Lee KK, Stites WE, Lattman EE, et al. (2002) Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration. Biophys J 82: 3289-3304.
-
(2002)
Biophys J
, vol.82
, pp. 3289-3304
-
-
Fitch, C.A.1
Karp, D.A.2
Lee, K.K.3
Stites, W.E.4
Lattman, E.E.5
-
21
-
-
0034700307
-
pH dependence of stability of staphylococcal nuclease: Evidence of substantial electrostatic interactions in the denatured state
-
Whitten ST, Garcia-Moreno B, (2000) pH dependence of stability of staphylococcal nuclease: Evidence of substantial electrostatic interactions in the denatured state. Biochemistry 39: 14292-14304.
-
(2000)
Biochemistry
, vol.39
, pp. 14292-14304
-
-
Whitten, S.T.1
Garcia-Moreno, B.2
-
24
-
-
23144457576
-
H++: a server for estimating pK(a)s and adding missing hydrogens to macromolecules
-
Gordon JC, Myers JB, Folta T, Shoja V, Heath LS, et al. (2005) H++: a server for estimating pK(a)s and adding missing hydrogens to macromolecules. Nucleic Acids Research 33: W368-W371.
-
(2005)
Nucleic Acids Research
, vol.33
-
-
Gordon, J.C.1
Myers, J.B.2
Folta, T.3
Shoja, V.4
Heath, L.S.5
-
26
-
-
84986486656
-
A Rapid Finite-Difference Algorithm, Utilizing Successive over-Relaxation to Solve the Poisson-Boltzmann Equation
-
Nicholls A, Honig B, (1991) A Rapid Finite-Difference Algorithm, Utilizing Successive over-Relaxation to Solve the Poisson-Boltzmann Equation. Journal of Computational Chemistry 12: 435-445.
-
(1991)
Journal of Computational Chemistry
, vol.12
, pp. 435-445
-
-
Nicholls, A.1
Honig, B.2
-
27
-
-
0025398721
-
What If - a Molecular Modeling and Drug Design Program
-
Vriend G, (1990) What If- a Molecular Modeling and Drug Design Program. Journal of Molecular Graphics 8: 52-56.
-
(1990)
Journal of Molecular Graphics
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
28
-
-
79951476387
-
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pK(a) Predictions
-
Olsson MHM, Sondergaard CR, Rostkowski M, Jensen JH, (2011) PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pK(a) Predictions. Journal of Chemical Theory and Computation 7: 525-537.
-
(2011)
Journal of Chemical Theory and Computation
, vol.7
, pp. 525-537
-
-
Olsson, M.H.M.1
Sondergaard, C.R.2
Rostkowski, M.3
Jensen, J.H.4
-
30
-
-
85050521214
-
Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations
-
Madura JD, Davis ME, Gilson MK, Wade RC, Luty BA, et al. (1994) Biological Applications of Electrostatic Calculations and Brownian Dynamics Simulations. Reviews in Computational Chemistry V 5: 229-267.
-
(1994)
Reviews in Computational Chemistry V
, vol.5
, pp. 229-267
-
-
Madura, J.D.1
Davis, M.E.2
Gilson, M.K.3
Wade, R.C.4
Luty, B.A.5
-
31
-
-
0027477251
-
Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins
-
Gilson MK, (1993) Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins 15: 266-282.
-
(1993)
Proteins
, vol.15
, pp. 266-282
-
-
Gilson, M.K.1
-
32
-
-
81055157735
-
MCCE analysis of the pK(a) s of introduced buried acids and bases in staphylococcal nuclease
-
Gunner MR, Zhu X, Klein MC, (2011) MCCE analysis of the pK(a) s of introduced buried acids and bases in staphylococcal nuclease. Proteins 79: 3306-3319.
-
(2011)
Proteins
, vol.79
, pp. 3306-3319
-
-
Gunner, M.R.1
Zhu, X.2
Klein, M.C.3
-
33
-
-
81055157980
-
Calculation of pK(a) in proteins with the microenvironment modulated-screened coulomb potential
-
Shan J, Mehler EL, (2011) Calculation of pK(a) in proteins with the microenvironment modulated-screened coulomb potential. Proteins 79: 3346-3355.
-
(2011)
Proteins
, vol.79
, pp. 3346-3355
-
-
Shan, J.1
Mehler, E.L.2
-
34
-
-
81055140448
-
Is the prediction of pK(a) values by constant-pH molecular dynamics being hindered by inherited problems?
-
Machuqueiro M, Baptista AM, (2011) Is the prediction of pK(a) values by constant-pH molecular dynamics being hindered by inherited problems? Proteins 79: 3437-3447.
-
(2011)
Proteins
, vol.79
, pp. 3437-3447
-
-
Machuqueiro, M.1
Baptista, A.M.2
-
35
-
-
23244440384
-
Constant pH molecular dynamics with proton tautomerism
-
Khandogin J, Brooks CL III, (2005) Constant pH molecular dynamics with proton tautomerism. Biophys J 89: 141-157.
-
(2005)
Biophys J
, vol.89
, pp. 141-157
-
-
Khandogin, J.1
Brooks III, C.L.2
-
36
-
-
79952994820
-
Web Servers and Services for Electrostatics Calculations with APBS and PDB2PQR
-
Unni S, Huang Y, Hanson RM, Tobias M, Krishnan S, et al. (2011) Web Servers and Services for Electrostatics Calculations with APBS and PDB2PQR. Journal of Computational Chemistry 32: 1488-1491.
-
(2011)
Journal of Computational Chemistry
, vol.32
, pp. 1488-1491
-
-
Unni, S.1
Huang, Y.2
Hanson, R.M.3
Tobias, M.4
Krishnan, S.5
-
37
-
-
33846076119
-
Modeling electrostatic effects in proteins
-
Warshel A, Sharma PK, Kato M, Parson WW, (2006) Modeling electrostatic effects in proteins. Biochimica Et Biophysica Acta-Proteins and Proteomics 1764: 1647-1676.
-
(2006)
Biochimica Et Biophysica Acta-Proteins and Proteomics
, vol.1764
, pp. 1647-1676
-
-
Warshel, A.1
Sharma, P.K.2
Kato, M.3
Parson, W.W.4
-
38
-
-
33846614924
-
Analysing the pH-dependent properties of proteins using pKa calculations
-
Nielsen JE, (2007) Analysing the pH-dependent properties of proteins using pKa calculations. J Mol Graph Model 25: 691-699.
-
(2007)
J Mol Graph Model
, vol.25
, pp. 691-699
-
-
Nielsen, J.E.1
-
39
-
-
59649095261
-
Analyzing Enzymatic Ph Activity Profiles and Protein Titration Curves Using Structure-Based Pk(a) Calculations and Titration Curve Fitting
-
Nielsen JE, (2009) Analyzing Enzymatic Ph Activity Profiles and Protein Titration Curves Using Structure-Based Pk(a) Calculations and Titration Curve Fitting. Methods in Enzymology: Computer Methods Vol 454, Pt A 454: 233-258.
-
(2009)
Methods in Enzymology: Computer Methods
, vol.454
, Issue.Pt A454
, pp. 233-258
-
-
Nielsen, J.E.1
-
40
-
-
16244366490
-
Electrostatic interactions contribute to reduced heat capacity change of unfolding in a thermophilic ribosomal protein l30e
-
Lee CF, Allen MD, Bycroft M, Wong KB, (2005) Electrostatic interactions contribute to reduced heat capacity change of unfolding in a thermophilic ribosomal protein l30e. J Mol Biol 348: 419-431.
-
(2005)
J Mol Biol
, vol.348
, pp. 419-431
-
-
Lee, C.F.1
Allen, M.D.2
Bycroft, M.3
Wong, K.B.4
-
41
-
-
0037972269
-
Solution structure and thermal stability of ribosomal protein L30e from hyperthermophilic archaeon Thermococcus celer
-
Wong KB, Lee CF, Chan SH, Leung TY, Chen YW, et al. (2003) Solution structure and thermal stability of ribosomal protein L30e from hyperthermophilic archaeon Thermococcus celer. Protein Sci 12: 1483-1495.
-
(2003)
Protein Sci
, vol.12
, pp. 1483-1495
-
-
Wong, K.B.1
Lee, C.F.2
Chan, S.H.3
Leung, T.Y.4
Chen, Y.W.5
-
42
-
-
79959612799
-
Stabilizing salt-bridge enhances protein thermostability by reducing the heat capacity change of unfolding
-
Chan CH, Yu TH, Wong KB, (2011) Stabilizing salt-bridge enhances protein thermostability by reducing the heat capacity change of unfolding. PLoS One 6: e21624.
-
(2011)
PLoS One
, vol.6
-
-
Chan, C.H.1
Yu, T.H.2
Wong, K.B.3
-
43
-
-
29344472867
-
Effects of charge-to-alanine substitutions on the stability of ribosomal protein L30e from Thermococcus celer
-
Lee CF, Makhatadze GI, Wong KB, (2005) Effects of charge-to-alanine substitutions on the stability of ribosomal protein L30e from Thermococcus celer. Biochemistry 44: 16817-16825.
-
(2005)
Biochemistry
, vol.44
, pp. 16817-16825
-
-
Lee, C.F.1
Makhatadze, G.I.2
Wong, K.B.3
-
44
-
-
0003187567
-
The atomic structure of protein-protein recognition sites
-
Lo Conte L, Chothia C, Janin J, (1999) The atomic structure of protein-protein recognition sites. J Mol Biol 285: 2177-2198.
-
(1999)
J Mol Biol
, vol.285
, pp. 2177-2198
-
-
Lo Conte, L.1
Chothia, C.2
Janin, J.3
-
45
-
-
1842526110
-
The impact of Lys→Arg surface mutations on the crystallization of the globular domain of RhoGDI
-
Czepas J, Devedjiev Y, Krowarsch D, Derewenda U, Otlewski J, et al. (2004) The impact of Lys→Arg surface mutations on the crystallization of the globular domain of RhoGDI. Acta Crystallogr D Biol Crystallogr 60: 275-280.
-
(2004)
Acta Crystallogr D Biol Crystallogr
, vol.60
, pp. 275-280
-
-
Czepas, J.1
Devedjiev, Y.2
Krowarsch, D.3
Derewenda, U.4
Otlewski, J.5
-
46
-
-
0015507243
-
Mathematical models for interacting groups in nuclear magnetic resonance titration curves
-
Shrager RI, Cohen JS, Heller SR, Sachs DH, Schechter AN, (1972) Mathematical models for interacting groups in nuclear magnetic resonance titration curves. Biochemistry 11: 541-547.
-
(1972)
Biochemistry
, vol.11
, pp. 541-547
-
-
Shrager, R.I.1
Cohen, J.S.2
Heller, S.R.3
Sachs, D.H.4
Schechter, A.N.5
-
47
-
-
38048998514
-
Determination of electrostatic interaction energies and protonation state populations in enzyme active sites
-
Sondergaard CR, McIntosh LP, Pollastri G, Nielsen JE, (2008) Determination of electrostatic interaction energies and protonation state populations in enzyme active sites. J Mol Biol 376: 269-287.
-
(2008)
J Mol Biol
, vol.376
, pp. 269-287
-
-
Sondergaard, C.R.1
McIntosh, L.P.2
Pollastri, G.3
Nielsen, J.E.4
-
48
-
-
84855968560
-
-
NMR and X-ray Evidence That the HIV Protease Catalytic Aspartyl Groups Are Protonated in the Complex Formed by the Protease and a Non-Peptide Cyclic Urea-Based Inhibitor
-
Yamazaki T, Nicholson LK, Wingfield P, Stahl SJ, Kaufman JD, et al. (1994) NMR and X-ray Evidence That the HIV Protease Catalytic Aspartyl Groups Are Protonated in the Complex Formed by the Protease and a Non-Peptide Cyclic Urea-Based Inhibitor.
-
(1994)
-
-
Yamazaki, T.1
Nicholson, L.K.2
Wingfield, P.3
Stahl, S.J.4
Kaufman, J.D.5
-
49
-
-
0030596513
-
Cold denaturation of barstar: 1H, 15N and 13C NMR assignment and characterisation of residual structure
-
Wong KB, Freund SM, Fersht AR, (1996) Cold denaturation of barstar: 1H, 15N and 13C NMR assignment and characterisation of residual structure. J Mol Biol 259: 805-818.
-
(1996)
J Mol Biol
, vol.259
, pp. 805-818
-
-
Wong, K.B.1
Freund, S.M.2
Fersht, A.R.3
-
50
-
-
0347383758
-
Modeller: generation and refinement of homology-based protein structure models
-
Fiser A, Sali A, (2003) Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 374: 461-491.
-
(2003)
Methods Enzymol
, vol.374
, pp. 461-491
-
-
Fiser, A.1
Sali, A.2
|