-
1
-
-
0034039797
-
Electrostatic aspects of protein-protein interactions
-
DOI 10.1016/S0959-440X(00)00065-8
-
F.B. Sheinerman, R. Norel, and B. Honig Electrostatic aspects of protein-protein interactions Curr. Opin. Struct. Biol. 10 2000 153 159 (Pubitemid 30198940)
-
(2000)
Current Opinion in Structural Biology
, vol.10
, Issue.2
, pp. 153-159
-
-
Sheinerman, F.B.1
Norel, R.2
Honig, B.3
-
3
-
-
81055156035
-
Simulating electrostatic energies in proteins: Perspectives and some recent studies of pKas, redox, and other crucial functional properties
-
A. Warshel, and A. Dryga Simulating electrostatic energies in proteins: perspectives and some recent studies of pKas, redox, and other crucial functional properties Proteins 79 2011 3469 3484
-
(2011)
Proteins
, vol.79
, pp. 3469-3484
-
-
Warshel, A.1
Dryga, A.2
-
4
-
-
79551474943
-
In silico modeling of pH-optimum of protein-protein binding
-
R.C. Mitra, Z. Zhang, and E. Alexov In silico modeling of pH-optimum of protein-protein binding Proteins 79 2011 925 936
-
(2011)
Proteins
, vol.79
, pp. 925-936
-
-
Mitra, R.C.1
Zhang, Z.2
Alexov, E.3
-
5
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
DOI 10.1021/jm050362n
-
G.L. Warren, and C.W. Andrews M.S. Head A critical assessment of docking programs and scoring functions J. Med. Chem. 49 2006 5912 5931 (Pubitemid 44484938)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.-M.3
Clarke, B.4
LaLonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
6
-
-
35448990795
-
Computational methods for biomolecular electrostatics
-
F. Dong, B. Olsen, and N.A. Baker Computational methods for biomolecular electrostatics Methods Cell Biol. 84 2008 843 870
-
(2008)
Methods Cell Biol.
, vol.84
, pp. 843-870
-
-
Dong, F.1
Olsen, B.2
Baker, N.A.3
-
7
-
-
81055157092
-
On the development of protein pKa calculation algorithms
-
T. Carstensen, and D. Farrell J.E. Nielsen On the development of protein pKa calculation algorithms Proteins 79 2011 3287 3298
-
(2011)
Proteins
, vol.79
, pp. 3287-3298
-
-
Carstensen, T.1
Farrell, D.2
Nielsen, J.E.3
-
8
-
-
0027563464
-
On the calculation of pKas in proteins
-
A.-S. Yang, and M.R. Gunner B. Honig 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
Honig, B.3
-
11
-
-
0036787760
-
Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins
-
R.E. Georgescu, E.G. Alexov, and M.R. Gunner 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
-
12
-
-
0036099192
-
a values of buried residues: Analysis with continuum methods and role of water penetration
-
C.A. Fitch, and D.A. Karp B. García-Moreno E Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration Biophys. J. 82 2002 3289 3304 (Pubitemid 34547672)
-
(2002)
Biophysical Journal
, vol.82
, Issue.6
, pp. 3289-3304
-
-
Fitch, C.A.1
Karp, D.A.2
Lee, K.K.3
Stites, W.E.4
Lattman, E.E.5
Bertrand Garcia-Moreno, E.6
-
13
-
-
62749167980
-
MCCE2: Improving protein pKa calculations with extensive side chain rotamer sampling
-
Y. Song, J. Mao, and M.R. Gunner MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling J. Comput. Chem. 30 2009 2231 2247
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 2231-2247
-
-
Song, Y.1
Mao, J.2
Gunner, M.R.3
-
14
-
-
0034636803
-
Insensitivity of perturbed carboxyl pK(a) values in the ovomucoid third domain to charge replacement at a neighboring residue
-
DOI 10.1021/bi992967p
-
W.R. Forsyth, and A.D. Robertson Insensitivity of perturbed carboxyl pK(a) values in the ovomucoid third domain to charge replacement at a neighboring residue Biochemistry 39 2000 8067 8072 (Pubitemid 30452382)
-
(2000)
Biochemistry
, vol.39
, Issue.27
, pp. 8067-8072
-
-
Forsyth, W.R.1
Robertson, A.D.2
-
15
-
-
1842607440
-
a Calculations with Explicit and Implicit Solvent Models
-
DOI 10.1021/ja039788m
-
T. Simonson, J. Carlsson, and D.A. Case Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models J. Am. Chem. Soc. 126 2004 4167 4180 (Pubitemid 38453876)
-
(2004)
Journal of the American Chemical Society
, vol.126
, Issue.13
, pp. 4167-4180
-
-
Simonson, T.1
Carlsson, J.2
Case, D.A.3
-
16
-
-
8444247565
-
Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations
-
B. Kuhn, P.A. Kollman, and M. Stahl Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations J. Comput. Chem. 25 2004 1865 1872
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1865-1872
-
-
Kuhn, B.1
Kollman, P.A.2
Stahl, M.3
-
17
-
-
33747131772
-
Toward the accurate first-principles prediction of ionization equilibria in proteins
-
DOI 10.1021/bi060706r
-
J. Khandogin, and C.L. Brooks 3rd Toward the accurate first-principles prediction of ionization equilibria in proteins Biochemistry 45 2006 9363 9373 (Pubitemid 44223241)
-
(2006)
Biochemistry
, vol.45
, Issue.31
, pp. 9363-9373
-
-
Khandogin, J.1
Brooks III, C.L.2
-
18
-
-
80051643867
-
Continuous constant pH molecular dynamics in explicit solvent with pH-based replica exchange
-
J.A. Wallace, and J.K. Shen Continuous constant pH molecular dynamics in explicit solvent with pH-based replica exchange J. Chem. Theory Comput. 7 2011 2617 2629
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 2617-2629
-
-
Wallace, J.A.1
Shen, J.K.2
-
19
-
-
81055155931
-
PH replica-exchange method based on discrete protonation states
-
S.G. Itoh, A. Damjanović, and B.R. Brooks pH replica-exchange method based on discrete protonation states Proteins 79 2011 3420 3436
-
(2011)
Proteins
, vol.79
, pp. 3420-3436
-
-
Itoh, S.G.1
Damjanović, A.2
Brooks, B.R.3
-
20
-
-
81055156171
-
Measuring the successes and deficiencies of constant pH molecular dynamics: A blind prediction study
-
S.L. Williams, P.G. Blachly, and J.A. McCammon Measuring the successes and deficiencies of constant pH molecular dynamics: a blind prediction study Proteins 79 2011 3381 3388
-
(2011)
Proteins
, vol.79
, pp. 3381-3388
-
-
Williams, S.L.1
Blachly, P.G.2
McCammon, J.A.3
-
22
-
-
34548059996
-
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules
-
P. Schaefer, D. Riccardi, and Q. Cui Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules J. Chem. Phys. 123 2005 014905
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 014905
-
-
Schaefer, P.1
Riccardi, D.2
Cui, Q.3
-
23
-
-
0037963208
-
An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants
-
DOI 10.1002/prot.10332
-
M.S. Wisz, and H.W. Hellinga An empirical model for electrostatic interactions in proteins incorporating multiple geometry-dependent dielectric constants Proteins 51 2003 360 377 (Pubitemid 36528822)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.51
, Issue.3
, pp. 360-377
-
-
Wisz, M.S.1
Hellinga, H.W.2
-
25
-
-
79951476387
-
PROPKA3: Consistent treatment of internal and surface residues in empirical pKa predictions
-
M.H.M. Olsson, and C.R. Sondergaard J.H. Jensen PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions J. Chem. Theory Comput. 7 2011 525 537
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 525-537
-
-
Olsson, M.H.M.1
Sondergaard, C.R.2
Jensen, J.H.3
-
27
-
-
67650264153
-
Predicting protein pK(a) by environment similarity
-
F. Milletti, L. Storchi, and G. Cruciani Predicting protein pK(a) by environment similarity Proteins 76 2009 484 495
-
(2009)
Proteins
, vol.76
, pp. 484-495
-
-
Milletti, F.1
Storchi, L.2
Cruciani, G.3
-
28
-
-
73849104238
-
A fast and accurate method for predicting pKa of residues in proteins
-
R.-B. Huang, and Q.-S. Du K.C. Chou A fast and accurate method for predicting pKa of residues in proteins Protein Eng. Des. Sel. 23 2010 35 42
-
(2010)
Protein Eng. Des. Sel.
, vol.23
, pp. 35-42
-
-
Huang, R.-B.1
Du, Q.-S.2
Chou, K.C.3
-
29
-
-
0028859420
-
Conformation and hydrogen ion titration of proteins: A continuum electrostatic model with conformational flexibility
-
T.J. You, and D. Bashford Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility Biophys. J. 69 1995 1721 1733
-
(1995)
Biophys. J.
, vol.69
, pp. 1721-1733
-
-
You, T.J.1
Bashford, D.2
-
30
-
-
0031670370
-
Improving the accuracy of protein pK(a) calculations: Conformational averaging versus the average structure
-
DOI 10.1002/(SICI)1097-0134(19981101)33:2<145::AID-PROT1>3.0.CO;2-I
-
H.W.T. van Vlijmen, M. Schaefer, and M. Karplus Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure Proteins 33 1998 145 158 (Pubitemid 28457969)
-
(1998)
Proteins: Structure, Function and Genetics
, vol.33
, Issue.2
, pp. 145-158
-
-
Van Vlijmen, H.W.T.1
Schaefer, M.2
Karplus, M.3
-
31
-
-
81055156295
-
Developing hybrid approaches to predict pKa values of ionizable groups
-
S. Witham, and K. Talley E. Alexov Developing hybrid approaches to predict pKa values of ionizable groups Proteins 79 2011 3389 3399
-
(2011)
Proteins
, vol.79
, pp. 3389-3399
-
-
Witham, S.1
Talley, K.2
Alexov, E.3
-
32
-
-
33748400070
-
Including side chain flexibility in continuum electrostatic calculations of protein titration
-
P. Beroza, and D.A. Case Including side chain flexibility in continuum electrostatic calculations of protein titration J. Phys. Chem. 100 1996 20156 20163 (Pubitemid 126786945)
-
(1996)
Journal of Physical Chemistry
, vol.100
, Issue.51
, pp. 20156-20163
-
-
Beroza, P.1
Case, D.A.2
-
33
-
-
24944493938
-
Biochemistry: Toward high-resolution de novo structure prediction for small proteins
-
DOI 10.1126/science.1113801
-
P. Bradley, K.M.S. Misura, and D. Baker Toward high-resolution de novo structure prediction for small proteins Science 309 2005 1868 1871 (Pubitemid 41325099)
-
(2005)
Science
, vol.309
, Issue.5742
, pp. 1868-1871
-
-
Bradley, P.1
Misura, K.M.S.2
Baker, D.3
-
34
-
-
77957966065
-
A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19
-
A. Sircar, and S. Chaudhury J.J. Gray A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19 Proteins 78 2010 3115 3123
-
(2010)
Proteins
, vol.78
, pp. 3115-3123
-
-
Sircar, A.1
Chaudhury, S.2
Gray, J.J.3
-
35
-
-
79961012919
-
Benchmarking and analysis of protein docking performance in Rosetta v3.2
-
S. Chaudhury, and M. Berrondo J.J. Gray Benchmarking and analysis of protein docking performance in Rosetta v3.2 PLoS ONE 6 2011 e22477
-
(2011)
PLoS ONE
, vol.6
, pp. 22477
-
-
Chaudhury, S.1
Berrondo, M.2
Gray, J.J.3
-
36
-
-
40449116114
-
De novo computational design of retro-aldol enzymes
-
DOI 10.1126/science.1152692
-
L. Jiang, and E.A. Althoff D. Baker De novo computational design of retro-aldol enzymes Science 319 2008 1387 1391 (Pubitemid 351354873)
-
(2008)
Science
, vol.319
, Issue.5868
, pp. 1387-1391
-
-
Jiang, L.1
Althoff, E.A.2
Clemente, F.R.3
Doyle, L.4
Rothlisberger, D.5
Zanghellini, A.6
Gallaher, J.L.7
Betker, J.L.8
Tanaka, F.9
Barbas III, C.F.10
Hilvert, D.11
Houk, K.N.12
Stoddard, B.L.13
Baker, D.14
-
37
-
-
43449098518
-
Kemp elimination catalysts by computational enzyme design
-
DOI 10.1038/nature06879, PII NATURE06879
-
D. Röthlisberger, and O. Khersonsky D. Baker Kemp elimination catalysts by computational enzyme design Nature 453 2008 190 195 (Pubitemid 351667979)
-
(2008)
Nature
, vol.453
, Issue.7192
, pp. 190-195
-
-
Rothlisberger, D.1
Khersonsky, O.2
Wollacott, A.M.3
Jiang, L.4
DeChancie, J.5
Betker, J.6
Gallaher, J.L.7
Althoff, E.A.8
Zanghellini, A.9
Dym, O.10
Albeck, S.11
Houk, K.N.12
Tawfik, D.S.13
Baker, D.14
-
38
-
-
35948969909
-
Structure prediction of protein-solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite
-
DOI 10.1021/ja074602v
-
K. Makrodimitris, and D.L. Masica J.J. Gray Structure prediction of protein-solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite J. Am. Chem. Soc. 129 2007 13713 13722 (Pubitemid 350071801)
-
(2007)
Journal of the American Chemical Society
, vol.129
, Issue.44
, pp. 13713-13722
-
-
Makrodimitris, K.1
Masica, D.L.2
Kim, E.T.3
Gray, J.J.4
-
39
-
-
77956246697
-
De novo design of peptide-calcite biomineralization systems
-
D.L. Masica, and S.B. Schrier J.J. Gray De novo design of peptide-calcite biomineralization systems J. Am. Chem. Soc. 132 2010 12252 12262
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 12252-12262
-
-
Masica, D.L.1
Schrier, S.B.2
Gray, J.J.3
-
40
-
-
1842577654
-
Computational redesign of protein-protein interaction specificity
-
DOI 10.1038/nsmb749
-
T. Kortemme, and L.A. Joachimiak D. Baker Computational redesign of protein-protein interaction specificity Nat. Struct. Mol. Biol. 11 2004 371 379 (Pubitemid 38436803)
-
(2004)
Nature Structural and Molecular Biology
, vol.11
, Issue.4
, pp. 371-379
-
-
Kortemme, T.1
Joachimiak, L.A.2
Bullock, A.N.3
Schuler, A.D.4
Stoddard, B.L.5
Baker, D.6
-
41
-
-
0345306764
-
Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
-
DOI 10.1126/science.1089427
-
B. Kuhlman, and G. Dantas D. Baker Design of a novel globular protein fold with atomic-level accuracy Science 302 2003 1364 1368 (Pubitemid 37452172)
-
(2003)
Science
, vol.302
, Issue.5649
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.C.3
Varani, G.4
Stoddard, B.L.5
Baker, D.6
-
42
-
-
0034641749
-
Native protein sequences are close to optimal for their structures
-
B. Kuhlman, and D. Baker Native protein sequences are close to optimal for their structures Proc. Natl. Acad. Sci. USA 97 2000 10383 10388
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 10383-10388
-
-
Kuhlman, B.1
Baker, D.2
-
43
-
-
0038161052
-
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
-
DOI 10.1016/S0022-2836(03)00670-3
-
J.J. Gray, and S. Moughon D. Baker Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations J. Mol. Biol. 331 2003 281 299 (Pubitemid 36870793)
-
(2003)
Journal of Molecular Biology
, vol.331
, Issue.1
, pp. 281-299
-
-
Gray, J.J.1
Moughon, S.2
Wang, C.3
Schueler-Furman, O.4
Kuhlman, B.5
Rohl, C.A.6
Baker, D.7
-
44
-
-
79955721644
-
Structure-guided forcefield optimization
-
Y. Song, and M. Tyka D. Baker Structure-guided forcefield optimization Proteins 79 2011 1898 1909
-
(2011)
Proteins
, vol.79
, pp. 1898-1909
-
-
Song, Y.1
Tyka, M.2
Baker, D.3
-
46
-
-
79551470095
-
Role of conformational sampling in computing mutation-induced changes in protein structure and stability
-
E.H. Kellogg, A. Leaver-Fay, and D. Baker Role of conformational sampling in computing mutation-induced changes in protein structure and stability Proteins 79 2011 830 838
-
(2011)
Proteins
, vol.79
, pp. 830-838
-
-
Kellogg, E.H.1
Leaver-Fay, A.2
Baker, D.3
-
47
-
-
81055156704
-
The pKa Cooperative: A collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins
-
J.E. Nielsen, M.R. Gunner, and B.E. García-Moreno The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins Proteins 79 2011 3249 3259
-
(2011)
Proteins
, vol.79
, pp. 3249-3259
-
-
Nielsen, J.E.1
Gunner, M.R.2
García-Moreno, B.E.3
-
48
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
R.L. Dunbrack Jr., and F.E. Cohen Bayesian statistical analysis of protein side-chain rotamer preferences Protein Sci. 6 1997 1661 1681 (Pubitemid 27333069)
-
(1997)
Protein Science
, vol.6
, Issue.8
, pp. 1661-1681
-
-
Dunbrack Jr., R.L.1
Cohen, F.E.2
-
49
-
-
0035957234
-
A novel view of pH titration in biomolecules
-
DOI 10.1021/bi002740q
-
A. Onufriev, D.A. Case, and G.M. Ullmann A novel view of pH titration in biomolecules Biochemistry 40 2001 3413 3419 (Pubitemid 32242797)
-
(2001)
Biochemistry
, vol.40
, Issue.12
, pp. 3413-3419
-
-
Onufriev, A.1
Case, D.A.2
Ullmann, G.M.3
-
50
-
-
78649776250
-
Estimating binding affinities by docking/scoring methods using variable protonation states
-
M.-S. Park, C. Gao, and H.A. Stern Estimating binding affinities by docking/scoring methods using variable protonation states Proteins 79 2011 304 314
-
(2011)
Proteins
, vol.79
, pp. 304-314
-
-
Park, M.-S.1
Gao, C.2
Stern, H.A.3
-
51
-
-
0033135638
-
Effective energy function for proteins in solution
-
DOI 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N
-
T. Lazaridis, and M. Karplus Effective energy function for proteins in solution Proteins 35 1999 133 152 (Pubitemid 29165128)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.35
, Issue.2
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
52
-
-
0032929780
-
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
-
DOI 10.1002/(SICI)1097-0134(19990101)34:1<82::AID-PROT7>3.0.CO;2-A
-
K.T. Simons, and I. Ruczinski D. Baker Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins Proteins 34 1999 82 95 (Pubitemid 29019533)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.34
, Issue.1
, pp. 82-95
-
-
Simons, K.T.1
Ruczinski, I.2
Kooperberg, C.3
Fox, B.A.4
Bystroff, C.5
Baker, D.6
-
53
-
-
0037470581
-
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
-
DOI 10.1016/S0022-2836(03)00021-4
-
T. Kortemme, A.V. Morozov, and D. Baker An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes J. Mol. Biol. 326 2003 1239 1259 (Pubitemid 36263395)
-
(2003)
Journal of Molecular Biology
, vol.326
, Issue.4
, pp. 1239-1259
-
-
Kortemme, T.1
Morozov, A.V.2
Baker, D.3
-
54
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, and S. Swaminathan CHARMM: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 1983 187 217
-
(1983)
J. Comput. 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
-
56
-
-
0032562210
-
Energetics of electron-transfer and protonation reactions of the quinones in the photosynthetic reaction center of Rhodopseudomonas viridis
-
DOI 10.1021/bi971921y
-
B. Rabenstein, G.M. Ullmann, and E.-W. Knapp Energetics of electron-transfer and protonation reactions of the quinones in the photosynthetic reaction center of Rhodopseudomonas viridis Biochemistry 37 1998 2488 2495 (Pubitemid 28119324)
-
(1998)
Biochemistry
, vol.37
, Issue.8
, pp. 2488-2495
-
-
Rabenstein, B.1
Ullmann, G.M.2
Knapp, E.-W.3
-
58
-
-
0035939953
-
Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate
-
DOI 10.1038/35090602
-
D.J. Vocadlo, and G.J. Davies S.G. Withers Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate Nature 412 2001 835 838 (Pubitemid 32801467)
-
(2001)
Nature
, vol.412
, Issue.6849
, pp. 835-838
-
-
Vocadlo, D.J.1
Davies, G.J.2
Laine, R.3
Withers, S.G.4
-
59
-
-
0029666454
-
13C-NMR study of Bacillus circulans xylanase
-
DOI 10.1021/bi9613234
-
L.P. McIntosh, and G. Hand S.G. Withers 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 (Pubitemid 26269910)
-
(1996)
Biochemistry
, vol.35
, Issue.31
, 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
-
60
-
-
81055157863
-
Protein electrostatics and pKa blind predictions; Contribution from empirical predictions of internal ionizable residues
-
M.H.M. Olsson Protein electrostatics and pKa blind predictions; contribution from empirical predictions of internal ionizable residues Proteins 79 2011 3333 3345
-
(2011)
Proteins
, vol.79
, pp. 3333-3345
-
-
Olsson, M.H.M.1
-
61
-
-
14644438345
-
Progress and challenges in high-resolution refinement of protein structure models
-
DOI 10.1002/prot.20376
-
K.M.S. Misura, and D. Baker Progress and challenges in high-resolution refinement of protein structure models Proteins 59 2005 15 29 (Pubitemid 40316474)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.59
, Issue.1
, pp. 15-29
-
-
Misura, K.M.S.1
Baker, D.2
-
62
-
-
48449094112
-
Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles
-
S. Chaudhury, and J.J. Gray Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles J. Mol. Biol. 381 2008 1068 1087
-
(2008)
J. Mol. Biol.
, vol.381
, pp. 1068-1087
-
-
Chaudhury, S.1
Gray, J.J.2
-
64
-
-
43049126500
-
a values
-
DOI 10.1110/ps.073397708
-
M.J. Harms, and J.L. Schlessman B. García-Moreno A buried lysine that titrates with a normal pKa: role of conformational flexibility at the protein-water interface as a determinant of pKa values Protein Sci. 17 2008 833 845 (Pubitemid 351629578)
-
(2008)
Protein Science
, vol.17
, Issue.5
, pp. 833-845
-
-
Harms, M.J.1
Schlessman, J.L.2
Chimenti, M.S.3
Sue, G.R.4
Damjanovic, A.5
Garcia-Moreno, E.B.6
-
66
-
-
77952354807
-
Conformational consequences of ionization of Lys, Asp, and Glu buried at position 66 in staphylococcal nuclease
-
D.A. Karp, M.R. Stahley, and B. García-Moreno Conformational consequences of ionization of Lys, Asp, and Glu buried at position 66 in staphylococcal nuclease Biochemistry 49 2010 4138 4146
-
(2010)
Biochemistry
, vol.49
, pp. 4138-4146
-
-
Karp, D.A.1
Stahley, M.R.2
García-Moreno, B.3
-
68
-
-
70349307220
-
Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease
-
C.A. Castañeda, and C.A. Fitch B.E. García-Moreno Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease Proteins 77 2009 570 588
-
(2009)
Proteins
, vol.77
, pp. 570-588
-
-
Castañeda, C.A.1
Fitch, C.A.2
García-Moreno, B.E.3
-
69
-
-
10044267947
-
Stabilization of internal charges in a protein: Water penetration or conformational change?
-
DOI 10.1529/biophysj.104.048454
-
V.P. Denisov, and J.L. Schlessman B. Halle Stabilization of internal charges in a protein: water penetration or conformational change? Biophys. J. 87 2004 3982 3994 (Pubitemid 39602903)
-
(2004)
Biophysical Journal
, vol.87
, Issue.6
, pp. 3982-3994
-
-
Denisov, V.P.1
Schlessman, J.L.2
Garcia-Moreno, E.B.3
Halle, B.4
-
70
-
-
67349203635
-
The pK(a) values of acidic and basic residues buried at the same internal location in a protein are governed by different factors
-
M.J. Harms, and C.A. Castañeda B. García-Moreno E The pK(a) values of acidic and basic residues buried at the same internal location in a protein are governed by different factors J. Mol. Biol. 389 2009 34 47
-
(2009)
J. Mol. Biol.
, vol.389
, pp. 34-47
-
-
Harms, M.J.1
Castañeda, C.A.2
García-Moreno, E.B.3
-
71
-
-
0033850087
-
High apparent dielectric constants in the interior of a protein reflect water penetration
-
J.J. Dwyer, and A.G. Gittis B. García-Moreno E High apparent dielectric constants in the interior of a protein reflect water penetration Biophys. J. 79 2000 1610 1620
-
(2000)
Biophys. J.
, vol.79
, pp. 1610-1620
-
-
Dwyer, J.J.1
Gittis, A.G.2
García-Moreno, E.B.3
-
72
-
-
33947683393
-
High apparent dielectric constant inside a protein reflects structural reorganization coupled to the ionization of an internal Asp
-
DOI 10.1529/biophysj.106.090266
-
D.A. Karp, and A.G. Gittis B. García-Moreno E High apparent dielectric constant inside a protein reflects structural reorganization coupled to the ionization of an internal Asp Biophys. J. 92 2007 2041 2053 (Pubitemid 46495267)
-
(2007)
Biophysical Journal
, vol.92
, Issue.6
, pp. 2041-2053
-
-
Karp, D.A.1
Gittis, A.G.2
Stahley, M.R.3
Fitch, C.A.4
Stites, W.E.5
Garcia-Moreno, E.B.6
-
73
-
-
81055157735
-
MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease
-
M.R. Gunner, X. Zhu, and M.C. Klein MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease Proteins 79 2011 3306 3319
-
(2011)
Proteins
, vol.79
, pp. 3306-3319
-
-
Gunner, M.R.1
Zhu, X.2
Klein, M.C.3
-
74
-
-
81055156172
-
Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol
-
Y. Song Exploring conformational changes coupled to ionization states using a hybrid Rosetta-MCCE protocol Proteins 79 2011 3356 3363
-
(2011)
Proteins
, vol.79
, pp. 3356-3363
-
-
Song, Y.1
-
75
-
-
37649005586
-
Highly accurate biomolecular electrostatics in continuum dielectric environments
-
Y.C. Zhou, M. Feig, and G.W. Wei Highly accurate biomolecular electrostatics in continuum dielectric environments J. Comput. Chem. 29 2008 87 97
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 87-97
-
-
Zhou, Y.C.1
Feig, M.2
Wei, G.W.3
-
77
-
-
0033862774
-
Salt effects on ionization equilibria of histidines in myoglobin
-
Y.-H. Kao, and C.A. Fitch B. García-Moreno E Salt effects on ionization equilibria of histidines in myoglobin Biophys. J. 79 2000 1637 1654
-
(2000)
Biophys. J.
, vol.79
, pp. 1637-1654
-
-
Kao, Y.-H.1
Fitch, C.A.2
García-Moreno, E.B.3
-
78
-
-
0036228118
-
Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein
-
DOI 10.1110/ps.4700102
-
K.K. Lee, C.A. Fitch, and B. García-Moreno E Distance dependence and salt sensitivity of pairwise, coulombic interactions in a protein Protein Sci. 11 2002 1004 1016 (Pubitemid 34441220)
-
(2002)
Protein Science
, vol.11
, Issue.5
, pp. 1004-1016
-
-
Lee, K.K.1
Fitch, C.A.2
Bertrand Garcia-Moreno, E.3
-
79
-
-
78650905964
-
ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
-
A. Leaver-Fay, and M. Tyka P. Bradley ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules Methods Enzymol. 487 2011 545 574
-
(2011)
Methods Enzymol.
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
Tyka, M.2
Bradley, P.3
-
81
-
-
0036783381
-
Variability in the pKa of histidine side-chains correlates with burial within proteins
-
DOI 10.1002/prot.10177
-
S.P. Edgcomb, and K.P. Murphy Variability in the pKa of histidine side-chains correlates with burial within proteins Proteins 49 2002 1 6 (Pubitemid 34983169)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.49
, Issue.1
, pp. 1-6
-
-
Edgcomb, S.P.1
Murphy, K.P.2
|