-
1
-
-
0030986177
-
Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement
-
Adams, P. D., N. S. Pannu, R. J. Read, and A. T. Brunger., 1997. Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc. Natl. Acad. Sci. USA. 94:5018-5023.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 5018-5023
-
-
Adams, P.D.1
Pannu, N.S.2
Read, R.J.3
Brunger, A.T.4
-
2
-
-
0041006449
-
-
Universität Karlsruhe, Germany
-
Ahlrichs, R., M. Bär, H.-P. Baron, R. Bauernschmitt, S. Böcker, M. Ehrig, K. Eichkorn, S. Elliott, F. Haase, M. Häser, H. Horn, C. Huber, C. Kölmel, M. Kollwitz, C. Ochsenfeld, H. Öhm, A. Schäfer, U. Schneider, O. Treutler, M. von Arnim, F. Weigend, P. Weis, and H. Weiss. 2000. TURBOMOLE. Universität Karlsruhe, Germany.
-
(2000)
TURBOMOLE
-
-
Ahlrichs, R.1
Bär, M.2
Baron, H.-P.3
Bauernschmitt, R.4
Böcker, S.5
Ehrig, M.6
Eichkorn, K.7
Elliott, S.8
Haase, F.9
Häser, M.10
Horn, H.11
Huber, C.12
Kölmel, C.13
Kollwitz, M.14
Ochsenfeld, C.15
Öhm, H.16
Schäfer, A.17
Schneider, U.18
Treutler, O.19
Von Arnim, M.20
Weigend, F.21
Weis, P.22
Weiss, H.23
more..
-
3
-
-
0344813785
-
EXAFS spectroscopy of heme-containing oxygenases and peroxidases
-
Andersson, L. A., and J. H. Dawson. 1991. EXAFS spectroscopy of heme-containing oxygenases and peroxidases. Struct. Bond. 74:1-40.
-
(1991)
Struct. Bond.
, vol.74
, pp. 1-40
-
-
Andersson, L.A.1
Dawson, J.H.2
-
4
-
-
4043060022
-
IV porphyrin complexes and their one-electron oxidized derivatives. Axial ligand effects
-
IV porphyrin complexes and their one-electron oxidized derivatives. Axial ligand effects. J. Phys. Chem. A. 101:2692-2701.
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 2692-2701
-
-
Antony, J.1
Grodzicki, M.2
Trautwein, A.X.3
-
5
-
-
84957665033
-
An object-oriented programming suite for electrostatic effects in biological molecules
-
Y. Ishikawa, R.R. Oldehoeft, J.V.W. Reynders, and M. Tholburn, editors. Springer, Berlin, Germany
-
Bashford, D. 1997. An object-oriented programming suite for electrostatic effects in biological molecules. In Scientific Computing in Object-Oriented Parallel Environments, Lecture Notes in Computer Science, Vol. 134. Y. Ishikawa, R.R. Oldehoeft, J.V.W. Reynders, and M. Tholburn, editors. Springer, Berlin, Germany. 233-240.
-
(1997)
Scientific Computing in Object-Oriented Parallel Environments, Lecture Notes in Computer Science
, vol.134
, pp. 233-240
-
-
Bashford, D.1
-
7
-
-
58149324166
-
A comparison of the accuracy of different functionals
-
Bauschlicher, C. W. 1995. A comparison of the accuracy of different functionals. Chem. Phys. Lett. 246:40-44.
-
(1995)
Chem. Phys. Lett.
, vol.246
, pp. 40-44
-
-
Bauschlicher, C.W.1
-
8
-
-
4243553426
-
Density-functional exchange-energy approximation with correct asymptotic behavior
-
Becke, A. 1988. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A. 38:3098-3100.
-
(1988)
Phys. Rev. A
, vol.38
, pp. 3098-3100
-
-
Becke, A.1
-
10
-
-
0037161809
-
The catalytic pathway of horseradish peroxidase at high resolution
-
Berglund, G. I., G. H. Carlsson, A. T. Smith, H. Szörke, A. Henriksen, and J. Hajdu. 2002. The catalytic pathway of horseradish peroxidase at high resolution. Nature. 417:463-468.
-
(2002)
Nature
, vol.417
, pp. 463-468
-
-
Berglund, G.I.1
Carlsson, G.H.2
Smith, A.T.3
Szörke, H.4
Henriksen, A.5
Hajdu, J.6
-
11
-
-
84986492477
-
Atomic charges derived from semiempirical methods
-
Besler, B. H., K. M. Merz, and P. A. Kollman. 1990. Atomic charges derived from semiempirical methods. J. Comput. Chem. 11:431-439.
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 431-439
-
-
Besler, B.H.1
Merz, K.M.2
Kollman, P.A.3
-
12
-
-
0037952979
-
High-resolution crystal structures and spectroscopy of native and compound I cytochrome c peroxidase
-
Bonagura, C. A., B. Bhaskar, H. Shimizu, H. Li, M. Sundaramoorthy, D. E. McRee, D. B. Goodin, and T. L. Poulos. 2003. High-resolution crystal structures and spectroscopy of native and compound I cytochrome c peroxidase. Biochemistry. 42:5600-5608.
-
(2003)
Biochemistry
, vol.42
, pp. 5600-5608
-
-
Bonagura, C.A.1
Bhaskar, B.2
Shimizu, H.3
Li, H.4
Sundaramoorthy, M.5
McRee, D.E.6
Goodin, D.B.7
Poulos, T.L.8
-
13
-
-
0001897686
-
Assessment of phase accuracy by cross validation: The free R-value. Methods and applications
-
Brünger, A. T. 1993. Assessment of phase accuracy by cross validation: the free R-value. Methods and applications. Acta Crystallogr. D49:24-36.
-
(1993)
Acta Crystallogr. D
, vol.49
, pp. 24-36
-
-
Brünger, A.T.1
-
14
-
-
0030864522
-
Crystallographic refinement by simulated annealing. Methods and applications
-
Brünger, A. T., and L. M. Rice. 1997. Crystallographic refinement by simulated annealing. Methods and applications. Meth. Enzymol. 277:243-269.
-
(1997)
Meth. Enzymol.
, vol.277
, pp. 243-269
-
-
Brünger, A.T.1
Rice, L.M.2
-
15
-
-
0003834618
-
-
Yale University, New Haven, CT
-
Brünger, A. T., P. D. Adams, G. M. Clore, W. L. Delano, P. Gros, R. W. Grosse-Kunstleve, J.-S. Jiang, J. Kuszewski, M. Niges, N. S. Pannu, R. J. Read, L. M. Rice, T. Simonson, and G. L. Warren. 2000. Crystallography and NMR System CNS, Ver. 1.0. Yale University, New Haven, CT.
-
(2000)
Crystallography and NMR System CNS, Ver. 1.0
-
-
Brünger, A.T.1
Adams, P.D.2
Clore, G.M.3
Delano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.-S.7
Kuszewski, J.8
Niges, M.9
Pannu, N.S.10
Read, R.J.11
Rice, L.M.12
Simonson, T.13
Warren, G.L.14
-
16
-
-
0021670303
-
X-ray absorption studies of intermediates in peroxidase activity
-
Chance, M., L. Powers, Y. Chiang, T. Poulos, G. R. Schonbaum, I. Yamazaki, and K. G. Paul. 1984. X-ray absorption studies of intermediates in peroxidase activity. Arch. Biochem. Biophys. 235:596-611.
-
(1984)
Arch. Biochem. Biophys.
, vol.235
, pp. 596-611
-
-
Chance, M.1
Powers, L.2
Chiang, Y.3
Poulos, T.4
Schonbaum, G.R.5
Yamazaki, I.6
Paul, K.G.7
-
17
-
-
0022552272
-
X-ray absorption studies of myoglobin peroxide reveal functional differences between globins and heme enzymes
-
Chance, M., L. Powers, C. Kumar, and B. Chance. 1986a. X-ray absorption studies of myoglobin peroxide reveal functional differences between globins and heme enzymes. Biochemistry. 25:1259-1265.
-
(1986)
Biochemistry
, vol.25
, pp. 1259-1265
-
-
Chance, M.1
Powers, L.2
Kumar, C.3
Chance, B.4
-
18
-
-
0023056543
-
Cytochrome c peroxidase compound ES is identical with horseradish peroxidase compound I in iron-ligand distances
-
Chance, M., L. Powers, T. Poulos, and B. Chance. 1986b. Cytochrome c peroxidase compound ES is identical with horseradish peroxidase compound I in iron-ligand distances. Biochemistry. 25:1266-1270.
-
(1986)
Biochemistry
, vol.25
, pp. 1266-1270
-
-
Chance, M.1
Powers, L.2
Poulos, T.3
Chance, B.4
-
20
-
-
0034634543
-
Formation of compound I in the reaction of native myoglobin with hydrogen peroxide
-
Egawa, T., H. Shimada, and Y. Ishimura. 2000. Formation of compound I in the reaction of native myoglobin with hydrogen peroxide. J. Biol. Chem. 275:34858-34866.
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 34858-34866
-
-
Egawa, T.1
Shimada, H.2
Ishimura, Y.3
-
21
-
-
22944484208
-
Auxiliary basis sets to approximate Coulomb potentials
-
Eichkorn, K., O. Treutler, H. Öhm, M. Häser, and R. Ahlrichs. 1995. Auxiliary basis sets to approximate Coulomb potentials. Chem. Phys. Lett. 240:283-290.
-
(1995)
Chem. Phys. Lett.
, vol.240
, pp. 283-290
-
-
Eichkorn, K.1
Treutler, O.2
Öhm, H.3
Häser, M.4
Ahlrichs, R.5
-
22
-
-
0031285825
-
Auxiliary basis sets for main row and transition metals and their use to approximate Coulomb potentials
-
Eichkorn, K., F. Weigend, O. Treutler, and R. Ahlrichs. 1997. Auxiliary basis sets for main row and transition metals and their use to approximate Coulomb potentials. Theor. Chim. Acta. 97:119-124.
-
(1997)
Theor. Chim. Acta
, vol.97
, pp. 119-124
-
-
Eichkorn, K.1
Weigend, F.2
Treutler, O.3
Ahlrichs, R.4
-
23
-
-
79952608525
-
Accurate bond and angle parameters for x-ray protein structure refinement
-
Engh, R. A., and R. Huber. 1991. Accurate bond and angle parameters for x-ray protein structure refinement. Acta Crystallogr. A47:392-400.
-
(1991)
Acta Crystallogr. A
, vol.47
, pp. 392-400
-
-
Engh, R.A.1
Huber, R.2
-
24
-
-
0024348254
-
pH-dependent forms of the ferryl heme in myoglobin peroxide analysed by variable-temperature magnetic circular dichroism
-
Foote, N., P. M. A. Gadsby, C. Greenwood, and A. J. Thompson. 1989. pH-dependent forms of the ferryl heme in myoglobin peroxide analysed by variable-temperature magnetic circular dichroism. J. Biol. Chem. 261:515-522.
-
(1989)
J. Biol. Chem.
, vol.261
, pp. 515-522
-
-
Foote, N.1
Gadsby, P.M.A.2
Greenwood, C.3
Thompson, A.J.4
-
25
-
-
84891154517
-
-
Gaussian Inc., Pittsburgh, PA
-
Frisch, M. J., G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, C. Gonzalez, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, M. Head-Gordon, E. S. Replogle, and J. A. Pople. 1998. GAUSSIAN 98, Rev. A.5. Gaussian Inc., Pittsburgh, PA.
-
(1998)
GAUSSIAN 98, Rev. A.5
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Zakrzewski, V.G.7
Montgomery, J.A.8
Stratmann, R.E.9
Burant, J.C.10
Dapprich, S.11
Millam, J.M.12
Daniels, A.D.13
Kudin, K.N.14
Strain, M.C.15
Farkas, O.16
Tomasi, J.17
Barone, V.18
Cossi, M.19
Cammi, R.20
Mennucci, B.21
Pomelli, C.22
Adamo, C.23
Clifford, S.24
Ochterski, J.25
Petersson, G.A.26
Ayala, P.Y.27
Cui, Q.28
Morokuma, K.29
Malick, D.K.30
Rabuck, A.D.31
Raghavachari, K.32
Foresman, J.B.33
Cioslowski, J.34
Ortiz, J.V.35
Stefanov, B.B.36
Liu, G.37
Liashenko, A.38
Piskorz, P.39
Komaromi, I.40
Gomperts, R.41
Martin, R.L.42
Fox, D.J.43
Keith, T.44
Al-Laham, M.A.45
Peng, C.Y.46
Nanayakkara, A.47
Gonzalez, C.48
Challacombe, M.49
Gill, P.M.W.50
Johnson, B.51
Chen, W.52
Wong, M.W.53
Andres, J.L.54
Head-Gordon, M.55
Replogle, E.S.56
Pople, J.A.57
more..
-
26
-
-
0344807313
-
Horseradish peroxidase
-
A. Messerschmidt, R. Huber, T. Poulos, and K. Wieghardt, editors. J. Wiley & Sons, Chichester, UK
-
Gajhede, M. 2001. Horseradish peroxidase. In Handbook of Metalloproteins, Vol. 1. A. Messerschmidt, R. Huber, T. Poulos, and K. Wieghardt, editors. J. Wiley & Sons, Chichester, UK. 195-209.
-
(2001)
Handbook of Metalloproteins
, vol.1
, pp. 195-209
-
-
Gajhede, M.1
-
27
-
-
33751158684
-
IV complexes, models of peroxidase compound I and II
-
IV complexes, models of peroxidase compound I and II. J. Phys. Chem. 98:5576-5579.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 5576-5579
-
-
Ghosh, A.1
Almlöf, J.2
Que, L.3
-
28
-
-
0028360918
-
Ferrylmyoglobin: Formation and chemical reactivity toward electron-donating compounds
-
Giulivi, C., and E. Cadenas. 1994. Ferrylmyoglobin: formation and chemical reactivity toward electron-donating compounds. Methods Enzymol. 233:189-202.
-
(1994)
Methods Enzymol.
, vol.233
, pp. 189-202
-
-
Giulivi, C.1
Cadenas, E.2
-
29
-
-
0029859337
-
Ferryl intermediates of catalase captured by time-resolved Weissenberg crystallography and UV-VIS spectroscopy
-
Gouet, P., H.-M. Jouve, P. A. Williams, I. Andersson, P. Adreoletti, L. Nussaume, and J. Hajdu. 1996. Ferryl intermediates of catalase captured by time-resolved Weissenberg crystallography and UV-VIS spectroscopy. Nat. Struct. Biol. 3:951-956.
-
(1996)
Nat. Struct. Biol.
, vol.3
, pp. 951-956
-
-
Gouet, P.1
Jouve, H.-M.2
Williams, P.A.3
Andersson, I.4
Adreoletti, P.5
Nussaume, L.6
Hajdu, J.7
-
30
-
-
0035913740
-
The structure and spin coupling of catalase compound I: A study of noncovalent effects
-
Green, M. T. 2001. The structure and spin coupling of catalase compound I: a study of noncovalent effects. J. Am. Chem. Soc. 123:9218-9219.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 9218-9219
-
-
Green, M.T.1
-
31
-
-
2942679678
-
Oxoiron(IV) in chloroperoxidase compound II is basic: Implications for P450 chemistry
-
Green, M. T., J. H. Dawson, and H. B. Gray. 2004. Oxoiron(IV) in chloroperoxidase compound II is basic: implications for P450 chemistry. Science. 304:1653-1656.
-
(2004)
Science
, vol.304
, pp. 1653-1656
-
-
Green, M.T.1
Dawson, J.H.2
Gray, H.B.3
-
32
-
-
0029737668
-
Structural factors governing hemin dissociation from met-myoglobin
-
Hargrove, M. S., A. J. Wilkinson, and J. S. Olson. 1996. Structural factors governing hemin dissociation from met-myoglobin. Biochemistry. 35:11300-11309.
-
(1996)
Biochemistry
, vol.35
, pp. 11300-11309
-
-
Hargrove, M.S.1
Wilkinson, A.J.2
Olson, J.S.3
-
33
-
-
0035606245
-
High-valent intermediates of heme proteins and model compounds
-
Harris, D. L. 2001. High-valent intermediates of heme proteins and model compounds. Curr. Opin. Chem. Biol. 5:724-735.
-
(2001)
Curr. Opin. Chem. Biol.
, vol.5
, pp. 724-735
-
-
Harris, D.L.1
-
34
-
-
0035100897
-
Proximal ligand effects on electronic structure and spectra of compound I of peroxidases
-
Harris, D. L., and G. H. Loew. 2001. Proximal ligand effects on electronic structure and spectra of compound I of peroxidases. J. Porph. Phtalocyanins. 5:334-344.
-
(2001)
J. Porph. Phtalocyanins
, vol.5
, pp. 334-344
-
-
Harris, D.L.1
Loew, G.H.2
-
35
-
-
84873055189
-
-
Wiley-Interscience, New York
-
Hehre, W. J., L. Radom, P. v. R. Schleyer, and J. A. Pople. 1986. Ab Initio Molecular Orbital Theory. Wiley-Interscience, New York.
-
(1986)
Ab Initio Molecular Orbital Theory
-
-
Hehre, W.J.1
Radom, L.2
Schleyer, P.V.R.3
Pople, J.A.4
-
36
-
-
0036941303
-
An iron hydroxide moiety in the 1.35 Å resolution structure of hydrogen peroxide derived myoglobin compound D at pH 5.2
-
Hersleth, H. P., B. Dalhus, C. H. Göbitz, and K. K. Andersson. 2002. An iron hydroxide moiety in the 1.35 Å resolution structure of hydrogen peroxide derived myoglobin compound D at pH 5.2. J. Biol. Inorg. Chem. 7:299-304.
-
(2002)
J. Biol. Inorg. Chem.
, vol.7
, pp. 299-304
-
-
Hersleth, H.P.1
Dalhus, B.2
Göbitz, C.H.3
Andersson, K.K.4
-
37
-
-
16344365416
-
Compound II in peroxidases: New resonance forms suggested by pH-dependent structures of myoglobin intermediates formed by oxidation with peroxides
-
Abstr.
-
Hersleth, H. P., B. Dalhus, C. H. Görbitz, and K. K. Andersson. 2001. Compound II in peroxidases: new resonance forms suggested by pH-dependent structures of myoglobin intermediates formed by oxidation with peroxides. J. Inorg. Biochem. 86:260. (Abstr.)
-
(2001)
J. Inorg. Biochem.
, vol.86
, pp. 260
-
-
Hersleth, H.P.1
Dalhus, B.2
Görbitz, C.H.3
Andersson, K.K.4
-
38
-
-
0031576963
-
On the parameterization of the local correlation functional. What is Becke-3-Lyp?
-
Hertwig, R. H., and W. Koch. 1997. On the parameterization of the local correlation functional. What is Becke-3-Lyp? Chem. Phys. Lett. 268:345-351.
-
(1997)
Chem. Phys. Lett.
, vol.268
, pp. 345-351
-
-
Hertwig, R.H.1
Koch, W.2
-
40
-
-
36949086829
-
Effect of drying upon the absorption spectra of hemoglobin and its derivatives
-
Keilin, D., and E. F. Hartree. 1950. Effect of drying upon the absorption spectra of hemoglobin and its derivatives. Nature. 166:513-518.
-
(1950)
Nature
, vol.166
, pp. 513-518
-
-
Keilin, D.1
Hartree, E.F.2
-
41
-
-
36949091243
-
Structure of myoglobin-three-dimensional Fourier synthesis at 2-Å resolution
-
Kendrew, J. C., R. E. Dickerson, B. E. Strandberg, R. G. Hart, D. R. Davies, D. C. Phillips, and V. C. Shore. 1960. Structure of myoglobin-three- dimensional Fourier synthesis at 2-Å resolution. Nature. 185:422-427.
-
(1960)
Nature
, vol.185
, pp. 422-427
-
-
Kendrew, J.C.1
Dickerson, R.E.2
Strandberg, B.E.3
Hart, R.G.4
Davies, D.R.5
Phillips, D.C.6
Shore, V.C.7
-
42
-
-
0032215320
-
Databases in protein crystallography
-
Kleywegt, G. J., and T. A. Jones. 1998. Databases in protein crystallography. Acta Crystallogr. D54:1119-1131.
-
(1998)
Acta Crystallogr. D
, vol.54
, pp. 1119-1131
-
-
Kleywegt, G.J.1
Jones, T.A.2
-
43
-
-
0031587459
-
Density functional study on the electronic structures of model peroxidase compounds I and II
-
Kuramochi, H., L. Noodleman, and D. A. Case. 1997. Density functional study on the electronic structures of model peroxidase compounds I and II. J. Am. Chem. Soc. 119:11442-11451.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 11442-11451
-
-
Kuramochi, H.1
Noodleman, L.2
Case, D.A.3
-
44
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics. Studies of proteins
-
MacKerell, A. D., D. M. Bashford, R. L. D. Bellott, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics. Studies of proteins. J. Phys. Chem. B. 102:3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.M.2
Bellott Jr., R.L.D.3
Evanseck, J.D.4
Field, M.J.5
Fischer, S.6
Gao, J.7
Guo, H.8
Ha, S.9
Joseph-McCarthy, D.10
Kuchnir, L.11
Kuczera, K.12
Lau, F.13
Mattos, C.14
Michnick, S.15
Ngo, T.16
Nguyen, D.T.17
Prodhom, B.18
Reiher, W.E.19
Roux, B.20
Schlenkrich, M.21
Smith, J.C.22
Stote, R.23
Straub, J.24
Watanabe, M.25
Wiorkiewicz-Kuczera, J.26
Yin, D.27
Karplus, M.28
more..
-
45
-
-
0033613928
-
Effect of the location of distal histidine in the reaction of myoglobin with hydrogen peroxide
-
Matsui, T., S. Ozaki, E. Liong, G. N. Phillips, and Y. Watanabe. 1999. Effect of the location of distal histidine in the reaction of myoglobin with hydrogen peroxide. J. Biol. Chem. 274:2838-2844.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 2838-2844
-
-
Matsui, T.1
Ozaki, S.2
Liong, E.3
Phillips, G.N.4
Watanabe, Y.5
-
46
-
-
1842426962
-
Peroxide-utilizing biocatalysts: Structural and functional diversity of heme-containing enzymes
-
Matsunaga, I., and Y. Shir. 2004. Peroxide-utilizing biocatalysts: structural and functional diversity of heme-containing enzymes. Curr. Opin. Chem. Biol. 8:127-132.
-
(2004)
Curr. Opin. Chem. Biol.
, vol.8
, pp. 127-132
-
-
Matsunaga, I.1
Shir, Y.2
-
47
-
-
0032711930
-
Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems
-
Monard, G., and K. M. Merz. 1999. Combined quantum mechanical/ molecular mechanical methodologies applied to biomolecular systems. Acc. Chem. Res. 32:904-911.
-
(1999)
Acc. Chem. Res.
, vol.32
, pp. 904-911
-
-
Monard, G.1
Merz, K.M.2
-
48
-
-
0035786390
-
The QM/MM approach to enzymatic reactions
-
L.A. Eriksson, editor. Elsevier Science, Amsterdam, The Netherlands
-
Mulholland, A. J. 2001. The QM/MM approach to enzymatic reactions. In Theoretical Biochemistry-Processes and Properties of Biological Systems, Theoretical and Computational Chemistry, Vol. 9. L.A. Eriksson, editor. Elsevier Science, Amsterdam, The Netherlands.
-
(2001)
Theoretical Biochemistry-Processes and Properties of Biological Systems, Theoretical and Computational Chemistry
, vol.9
-
-
Mulholland, A.J.1
-
49
-
-
1842868487
-
The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex
-
Murshudov, G. N., A. I. Grebenko, J. A. Brannigan, A. A. Antson, V. V. Barynin, G. G. Dodson, Z. Dauter, K. S. Wilson, and W. R. Melik-Adamyan. 2002. The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex. Acta Crystallogr. D58:1972-1982.
-
(2002)
Acta Crystallogr. D
, vol.58
, pp. 1972-1982
-
-
Murshudov, G.N.1
Grebenko, A.I.2
Brannigan, J.A.3
Antson, A.A.4
Barynin, V.V.5
Dodson, G.G.6
Dauter, Z.7
Wilson, K.S.8
Melik-Adamyan, W.R.9
-
50
-
-
0035625887
-
Quantum mechanical/molecular mechanical methods and the study of kinetic isotope effects: Modelling the covalent junction region and application to the enzyme xylose isomerase
-
Nicoll, R. M., S. A. Hindle, G. MacKenzie, I. H. Hillier, and N. A. Burton. 2001. Quantum mechanical/molecular mechanical methods and the study of kinetic isotope effects: modelling the covalent junction region and application to the enzyme xylose isomerase. Theor. Chim. Acta. 106:105-112.
-
(2001)
Theor. Chim. Acta
, vol.106
, pp. 105-112
-
-
Nicoll, R.M.1
Hindle, S.A.2
MacKenzie, G.3
Hillier, I.H.4
Burton, N.A.5
-
51
-
-
4444253515
-
Protonation status of protein ligands can be determined by quantum refinement
-
Nilsson, K., and U. Ryde. 2004. Protonation status of protein ligands can be determined by quantum refinement. J. Inorg. Biochem. 98:1539-1546.
-
(2004)
J. Inorg. Biochem.
, vol.98
, pp. 1539-1546
-
-
Nilsson, K.1
Ryde, U.2
-
52
-
-
0031167555
-
Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations
-
Nina, M., and B. Roux. 1997. Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations. J. Phys. Chem. B. 101:5239-5248.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 5239-5248
-
-
Nina, M.1
Roux, B.2
-
53
-
-
0030839466
-
Conversion of myoglobin into a peroxygenase: A catalytic intermediate of sulfoxidation and epoxidation by the F43H/H64L mutant
-
Ozaki, S., T. Matsui, and Y. Watanabe. 1997. Conversion of myoglobin into a peroxygenase: a catalytic intermediate of sulfoxidation and epoxidation by the F43H/H64L mutant. J. Am. Chem. Soc. 119:6666-6667.
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 6666-6667
-
-
Ozaki, S.1
Matsui, T.2
Watanabe, Y.3
-
54
-
-
0023768506
-
The resonance Raman spectrum of horseradish peroxidase compound I
-
Paeng, K. J., and J. R. Kincaid. 1988. The resonance Raman spectrum of horseradish peroxidase compound I. J. Am. Chem. Soc. 110:7913-7915.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 7913-7915
-
-
Paeng, K.J.1
Kincaid, J.R.2
-
55
-
-
0000649842
-
Improved structure refinement through maximum likelihood
-
Pannu, N. S., and R. J. Read. 1996. Improved structure refinement through maximum likelihood. Acta Ctystallogr. A52:659-668.
-
(1996)
Acta Ctystallogr. A
, vol.52
, pp. 659-668
-
-
Pannu, N.S.1
Read, R.J.2
-
56
-
-
33845376272
-
Structural characterization of horseradish peroxidase using EXAFS spectroscopy. Evidence for Fe=O ligation in compound I and II
-
Penner-Hahn, J. E., K. S. Eble, T. J. McMurry, M. Renner, A. L. Balch, J. T. Groves, and K. O. Hodgsen. 1986. Structural characterization of horseradish peroxidase using EXAFS spectroscopy. Evidence for Fe=O ligation in compound I and II. J. Am. Chem. Soc. 108:7819-7825.
-
(1986)
J. Am. Chem. Soc.
, vol.108
, pp. 7819-7825
-
-
Penner-Hahn, J.E.1
Eble, K.S.2
McMurry, T.J.3
Renner, M.4
Balch, A.L.5
Groves, J.T.6
Hodgsen, K.O.7
-
57
-
-
5944261746
-
Density-functional approximation for the correlation energy of the inhomogeneous electron gas
-
Perdew, J. P. 1986. Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys. Rev. B. 33:8822-8824.
-
(1986)
Phys. Rev. B
, vol.33
, pp. 8822-8824
-
-
Perdew, J.P.1
-
58
-
-
3342939208
-
Myoglobin
-
A. Messerschmidt, R. Huber, T. Poulos, and K. Wieghardt, editors. Wiley & Sons, Chichester, UK
-
Philips, G. N. 2001. Myoglobin. In Handbook of Metalloproteins, Vol. 1. A. Messerschmidt, R. Huber, T. Poulos, and K. Wieghardt, editors. Wiley & Sons, Chichester, UK. 5-15.
-
(2001)
Handbook of Metalloproteins
, vol.1
, pp. 5-15
-
-
Philips, G.N.1
-
59
-
-
0001851317
-
The role of the proximal ligand in heme enzymes
-
Poulos, T. L. 1996. The role of the proximal ligand in heme enzymes. J. Biol. Inorg. Chem. 1:356-359.
-
(1996)
J. Biol. Inorg. Chem.
, vol.1
, pp. 356-359
-
-
Poulos, T.L.1
-
60
-
-
0038171518
-
The proximal hydrogen-bonded residue controls the stability of the compound II intermediate of peroxidases and catalases
-
Rovira, C., and I. Fita. 2003. The proximal hydrogen-bonded residue controls the stability of the compound II intermediate of peroxidases and catalases. J. Phys. Chem. B. 107:5300-5305.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 5300-5305
-
-
Rovira, C.1
Fita, I.2
-
61
-
-
1542620864
-
On the role of the axial ligand in heme proteins - A theoretical study
-
Rydberg, P., E. Sigfridsson, and U. Ryde. 2004. On the role of the axial ligand in heme proteins-a theoretical study. J. Biol. Inorg. Chem. 9:203-223.
-
(2004)
J. Biol. Inorg. Chem.
, vol.9
, pp. 203-223
-
-
Rydberg, P.1
Sigfridsson, E.2
Ryde, U.3
-
62
-
-
0037304303
-
Combined quantum and molecular mechanics calculations on metalloproteins
-
Ryde, U. 2003. Combined quantum and molecular mechanics calculations on metalloproteins. Curr. Opin. Chem. Biol. 7:136-142.
-
(2003)
Curr. Opin. Chem. Biol.
, vol.7
, pp. 136-142
-
-
Ryde, U.1
-
63
-
-
0344012221
-
Quantum chemistry can improve protein crystal structures locally
-
Ryde, U., and K. Nilsson. 2003a. Quantum chemistry can improve protein crystal structures locally. J. Am. Chem. Soc. 125:14232-14233.
-
(2003)
J. Am. Chem. Soc.
, vol.125
, pp. 14232-14233
-
-
Ryde, U.1
Nilsson, K.2
-
64
-
-
0345227309
-
Quantum refinement - A combination of quantum chemistry and protein crystallography
-
Ryde, U., and K. Nilsson. 2003b. Quantum refinement - a combination of quantum chemistry and protein crystallography. J. Mol. Struct. 632:259-275.
-
(2003)
J. Mol. Struct.
, vol.632
, pp. 259-275
-
-
Ryde, U.1
Nilsson, K.2
-
65
-
-
0036667496
-
Quantum chemical geometry optimisations in proteins using crystallographic raw data
-
Ryde, U., L. Olsen, and K. Nilsson. 2002. Quantum chemical geometry optimisations in proteins using crystallographic raw data. J. Comput. Chem. 23:1058-1070.
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1058-1070
-
-
Ryde, U.1
Olsen, L.2
Nilsson, K.3
-
66
-
-
26344435738
-
Fully optimized contracted Gaussian basis set for atoms Li to Kr
-
Schäfer, A., H. Horn, and R. Ahlrichs. 1992. Fully optimized contracted Gaussian basis set for atoms Li to Kr. J. Chem. Phys. 97:2571-2577.
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 2571-2577
-
-
Schäfer, A.1
Horn, H.2
Ahlrichs, R.3
-
67
-
-
0034088779
-
450cam at atomic resolution
-
450cam at atomic resolution. Science. 287:1615-1622.
-
(2000)
Science
, vol.287
, pp. 1615-1622
-
-
Schlichting, I.1
Berendzen, J.2
Chu, K.3
Stock, A.M.4
Maves, S.A.5
Benson, D.E.6
Sweet, R.M.7
Ringe, D.8
Petsko, G.A.9
Sligar, S.G.10
-
68
-
-
0001363007
-
Transition-metal systems in biochemistry studied by high-accuracy quantum chemical methods
-
Siegbahn, P. E. M., and M. R. A. Blomberg. 2000. Transition-metal systems in biochemistry studied by high-accuracy quantum chemical methods. Chem. Rev. 100:421-437.
-
(2000)
Chem. Rev.
, vol.100
, pp. 421-437
-
-
Siegbahn, P.E.M.1
Blomberg, M.R.A.2
-
69
-
-
0035859440
-
A comparison of the inner-sphere reorganisation energies of cytochromes, iron-sulphur clusters, and blue copper proteins
-
Sigfridsson, E., M. H. M. Olsson, and U. Ryde. 2001. A comparison of the inner-sphere reorganisation energies of cytochromes, iron-sulphur clusters, and blue copper proteins. J. Phys. Chem. B. 105:5546-5552.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 5546-5552
-
-
Sigfridsson, E.1
Olsson, M.H.M.2
Ryde, U.3
-
70
-
-
0037329044
-
The importance of porphyrin distortions for the ferrochelatase reaction
-
Sigfridsson, E., and U. Ryde. 2003. The importance of porphyrin distortions for the ferrochelatase reaction. J. Biol. Inorg. Chem. 8:273-282.
-
(2003)
J. Biol. Inorg. Chem.
, vol.8
, pp. 273-282
-
-
Sigfridsson, E.1
Ryde, U.2
-
71
-
-
0021854541
-
Heme-linked ionization of horseradish peroxidase compound II monitored by the resonance Raman Fe(IV)=O stretching vibration
-
Sitter, A. J., C. M. Reczek, and J. Terner. 1985. Heme-linked ionization of horseradish peroxidase compound II monitored by the resonance Raman Fe(IV)=O stretching vibration. J. Biol. Chem. 260:7515-7522.
-
(1985)
J. Biol. Chem.
, vol.260
, pp. 7515-7522
-
-
Sitter, A.J.1
Reczek, C.M.2
Terner, J.3
-
72
-
-
0023806074
-
Resonance Raman spectroscopic evidence for heme iron-hydroxide ligation in peroxidase alkaline forms
-
Sitter, A. J., J. R. Shifflett, and J. Terner. 1988. Resonance Raman spectroscopic evidence for heme iron-hydroxide ligation in peroxidase alkaline forms. J. Biol. Chem. 263:13032-13038.
-
(1988)
J. Biol. Chem.
, vol.263
, pp. 13032-13038
-
-
Sitter, A.J.1
Shifflett, J.R.2
Terner, J.3
-
73
-
-
0032042908
-
Substrate binding and catalysis in heme peroxidases
-
Smith, A. T., and N. C. Veitch. 1998. Substrate binding and catalysis in heme peroxidases. Curr. Opin. Chem. Biol. 2:269-278.
-
(1998)
Curr. Opin. Chem. Biol.
, vol.2
, pp. 269-278
-
-
Smith, A.T.1
Veitch, N.C.2
-
74
-
-
0035110522
-
Is the CO adduct of myoglobin bent, and does it matter?
-
Spiro, T. G., and P. M. Kozlowski. 2001. Is the CO adduct of myoglobin bent, and does it matter? Acc. Chem. Res. 34:137-144.
-
(2001)
Acc. Chem. Res.
, vol.34
, pp. 137-144
-
-
Spiro, T.G.1
Kozlowski, P.M.2
-
75
-
-
0023656226
-
Autoxidation of oxymyoglobin an overall stoichiometry including subsequent side reactions
-
Tajima, G., and K. Shikama. 1987. Autoxidation of oxymyoglobin an overall stoichiometry including subsequent side reactions. J. Biol. Chem. 262:12603-12606.
-
(1987)
J. Biol. Chem.
, vol.262
, pp. 12603-12606
-
-
Tajima, G.1
Shikama, K.2
-
76
-
-
0030612614
-
a changes in a protein tyrosine phosphatase: Experimental and theoretical determination of electrostatic properties in a small protein
-
a changes in a protein tyrosine phosphatase: experimental and theoretical determination of electrostatic properties in a small protein. Biochemistry. 36:11984-11994.
-
(1997)
Biochemistry
, vol.36
, pp. 11984-11994
-
-
Tishmack, P.A.1
Bashford, D.2
Harms, E.3
Van Etten, R.I.4
-
78
-
-
0033520695
-
Reaction mechanism of compound I formation in heme peroxidases: A density functional theory study
-
Wirstam, M., M. R. A. Blomberg, and P. E. M. Siegbahn. 1999. Reaction mechanism of compound I formation in heme peroxidases: a density functional theory study. J. Am. Chem. Soc. 121:10178-10185.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 10178-10185
-
-
Wirstam, M.1
Blomberg, M.R.A.2
Siegbahn, P.E.M.3
|