-
1
-
-
0036285985
-
Molecular dynamics simulations of biomolecules
-
Karplus M. Molecular dynamics simulations of biomolecules. Acc. Chem. Res. 35:2002;321-323.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 321-323
-
-
Karplus, M.1
-
5
-
-
0034979318
-
Biomolecular simulations: Recent developments in force-fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions
-
In this review, applications of quantum mechanics as well as of MD and free energy calculation methods are discussed for the study of enzymatic catalysis and protein-protein and protein-ligand interactions.
-
Wang W., Donini O., Reyes C.M., Kollman P.A. Biomolecular simulations: recent developments in force-fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu. Rev. Biophys. Biomol. Struct. 30:2001;211-243 In this review, applications of quantum mechanics as well as of MD and free energy calculation methods are discussed for the study of enzymatic catalysis and protein-protein and protein-ligand interactions.
-
(2001)
Annu. Rev. Biophys. Biomol. Struct.
, vol.30
, pp. 211-243
-
-
Wang, W.1
Donini, O.2
Reyes, C.M.3
Kollman, P.A.4
-
6
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
This review presents a description of biomolecular simulations from their origin to the present applications, discussing the ever-increasing potential for contributing to biology.
-
Karplus M., McCammon J.A. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9:2002;646-652 This review presents a description of biomolecular simulations from their origin to the present applications, discussing the ever-increasing potential for contributing to biology.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
7
-
-
0025048105
-
Molecular dynamics simulations in biology
-
Karplus M. Molecular dynamics simulations in biology. Nature. 347:1990;631-639.
-
(1990)
Nature
, vol.347
, pp. 631-639
-
-
Karplus, M.1
-
8
-
-
84986532404
-
Calculation of molecular geometries, relative conformational energies, dipole moments, and molecular electrostatic potential fitted charges of small organic molecules of biochemical interest by density functional theory
-
St-Amant A., Cornell W.D., Halgren T.A., Kollman P.A. Calculation of molecular geometries, relative conformational energies, dipole moments, and molecular electrostatic potential fitted charges of small organic molecules of biochemical interest by density functional theory. J. Comp. Chem. 16:1995;1483.
-
(1995)
J. Comp. Chem.
, vol.16
, pp. 1483
-
-
St-Amant, A.1
Cornell, W.D.2
Halgren, T.A.3
Kollman, P.A.4
-
9
-
-
84946450438
-
Algorithms for macromolecular dynamics and constraint dynamics
-
Van Gunsteren W.F., Berendsen H.J.C. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34:1977;1311-1327.
-
(1977)
Mol. Phys.
, vol.34
, pp. 1311-1327
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
10
-
-
33645961739
-
A smooth particle-mesh-Ewald method
-
Essman V., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G. A smooth particle-mesh-Ewald method. J. Chem. Phys. 103:1995;8577-8593.
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essman, V.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
11
-
-
0035312820
-
New developments in applying quantum mechanics to proteins
-
The various strategies underlying the application of quantum mechanics to biomolecules are discussed.
-
Gogonea V., Suarez D., Van der Vaart A., Merz K.M. New developments in applying quantum mechanics to proteins. Curr. Opin. Struct. Biol. 11:2001;217-223 The various strategies underlying the application of quantum mechanics to biomolecules are discussed.
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 217-223
-
-
Gogonea, V.1
Suarez, D.2
Van der Vaart, A.3
Merz, K.M.4
-
12
-
-
0036286854
-
The role and perspective of ab initio molecular dynamics in the study of biological systems
-
This article describes the methodology for ab initio MD calculations, mostly based on DFT, in biological systems. It also discusses a few examples and provides a perspective for the advancement of the methodology.
-
Carloni P., Rothlisberger U., Parrinello M. The role and perspective of ab initio molecular dynamics in the study of biological systems. Acc. Chem. Res. 35:2002;455-464 This article describes the methodology for ab initio MD calculations, mostly based on DFT, in biological systems. It also discusses a few examples and provides a perspective for the advancement of the methodology.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 455-464
-
-
Carloni, P.1
Rothlisberger, U.2
Parrinello, M.3
-
13
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:1995;5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
14
-
-
0041784950
-
All atom empirical potential for molecular modeling and molecular dynamics studies of proteins
-
MacKerell A., Bashford D., Bellott M., Dumbrack R.L., Evanseck J.D., Field M.J., Gao H., Guo S., Ha S., Joseph D.et al. All atom empirical potential for molecular modeling and molecular dynamics studies of proteins. J. Phys. Chem. B. 102:1998;3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.1
Bashford, D.2
Bellott, M.3
Dumbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Gao, H.7
Guo, S.8
Ha, S.9
Joseph, D.10
-
15
-
-
0003544049
-
-
Zurich: Vdf Hochschulverlag
-
Van Gunsteren WF, Billeter SR, Eising AA, Hünenberger PH, Kruger P, Mark AE, Scott WRP, Tironi IG: Biomolecular Simulation: the Gromos96 Manual and User Guide. Zurich: Vdf Hochschulverlag; 1996.
-
(1996)
Biomolecular Simulation: The Gromos96 Manual and User Guide
-
-
Van Gunsteren, W.F.1
Billeter, S.R.2
Eising, A.A.3
Hünenberger, P.H.4
Kruger, P.5
Mark, A.E.6
Scott, W.R.P.7
Tironi, I.G.8
-
16
-
-
0036005957
-
Molecular modelling in structural biology
-
This review describes, in a simple and clear way, the various aspects of molecular modeling in structural biology, from the force fields and the MD program packages to structure determination and modeling.
-
Forster M.J. Molecular modelling in structural biology. Micron. 33:2002;365-384 This review describes, in a simple and clear way, the various aspects of molecular modeling in structural biology, from the force fields and the MD program packages to structure determination and modeling.
-
(2002)
Micron
, vol.33
, pp. 365-384
-
-
Forster, M.J.1
-
17
-
-
0035039453
-
The birth of computational structural biology
-
Levitt M. The birth of computational structural biology. Nat. Struct. Biol. 8:2001;392-393.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 392-393
-
-
Levitt, M.1
-
18
-
-
0036283096
-
Molecular dynamics and NMR spin relaxation in proteins
-
Case D.A. Molecular dynamics and NMR spin relaxation in proteins. Acc. Chem. Res. 35:2002;325-331.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 325-331
-
-
Case, D.A.1
-
19
-
-
0036051467
-
Hybrid QM/MM Car-Parrinello simulations of catalytic and enzymatic reactions
-
Colombo M.C., Guidoni L., Laio A., Magistrato A., Maurer P., Piana S., Rohehrig U., VandeVondele J., Zumstein M., Rothlisberger U. Hybrid QM/MM Car-Parrinello simulations of catalytic and enzymatic reactions. Chimia. 56:2002;11-17.
-
(2002)
Chimia
, vol.56
, pp. 11-17
-
-
Colombo, M.C.1
Guidoni, L.2
Laio, A.3
Magistrato, A.4
Maurer, P.5
Piana, S.6
Rohehrig, U.7
VandeVondele, J.8
Zumstein, M.9
Rothlisberger, U.10
-
20
-
-
0032711930
-
Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems
-
Monard G., Merz K.M. Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems. Acc. Chem. Res. 32:1999;904-911.
-
(1999)
Acc. Chem. Res.
, vol.32
, pp. 904-911
-
-
Monard, G.1
Merz, K.M.2
-
21
-
-
0017100947
-
Theoretical studies of enzymatic reactions:dielectric, electrostatic and steric stabilization of carbonium ion in the reaction of lysozyme
-
Warshel A., Levitt M. Theoretical studies of enzymatic reactions:dielectric, electrostatic and steric stabilization of carbonium ion in the reaction of lysozyme. J. Mol. Biol. 1036:1976;227-249.
-
(1976)
J. Mol. Biol.
, vol.1036
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
23
-
-
0036558223
-
A new molecular mechanics force field for the oxidized form of blue copper proteins
-
Comba P., Remenyi R. A new molecular mechanics force field for the oxidized form of blue copper proteins. J. Comp. Chem. 23:2002;697-705.
-
(2002)
J. Comp. Chem.
, vol.23
, pp. 697-705
-
-
Comba, P.1
Remenyi, R.2
-
25
-
-
0035125739
-
Deriving force field parameters for coordination complexes
-
Norrby P.-O., Brandt P. Deriving force field parameters for coordination complexes. Coord. Chem. Rev. 212:2001;79.
-
(2001)
Coord. Chem. Rev.
, vol.212
, pp. 79
-
-
Norrby, P.-O.1
Brandt, P.2
-
26
-
-
0035136601
-
The ligand field molecular mechanics model and the stereoelectronic effects of d and s electrons
-
Deeth R.J. The ligand field molecular mechanics model and the stereoelectronic effects of d and s electrons. Coord. Chem. Rev. 212:2001;11.
-
(2001)
Coord. Chem. Rev.
, vol.212
, pp. 11
-
-
Deeth, R.J.1
-
27
-
-
0012816341
-
Computational analysis of inorganic and bioinorganic nickel complexes
-
Edited by Banci L, Comba P. Dordrecht, The Netherlands: Kluwer
-
Csiki C, Norenberg KM, Shomaker CM, Zimmer M: Computational analysis of inorganic and bioinorganic nickel complexes. In Molecular Modeling and Dynamics of Bioinorganic Systems. Edited by Banci L, Comba P. Dordrecht, The Netherlands: Kluwer; 1997:105-130.
-
(1997)
Molecular Modeling and Dynamics of Bioinorganic Systems
, pp. 105-130
-
-
Csiki, C.1
Norenberg, K.M.2
Shomaker, C.M.3
Zimmer, M.4
-
28
-
-
0035849162
-
Parameters for the AMBER force field for the molecular mechanics modeling of the cobalt corrinoids
-
Marques H.M., Ngoma B., Egan T.J., Brown K.L. Parameters for the AMBER force field for the molecular mechanics modeling of the cobalt corrinoids. J. Mol. Struct. 561:2001;71-91.
-
(2001)
J. Mol. Struct.
, vol.561
, pp. 71-91
-
-
Marques, H.M.1
Ngoma, B.2
Egan, T.J.3
Brown, K.L.4
-
29
-
-
0033581183
-
Determination of two structural forms of catalytic bridging ligand in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation
-
Zhan C.-G., Souza O.N., Rittenhouse R.C., Ornstein R.L. Determination of two structural forms of catalytic bridging ligand in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation. J. Am. Chem. Soc. 121:1999;7279.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 7279
-
-
Zhan, C.-G.1
Souza, O.N.2
Rittenhouse, R.C.3
Ornstein, R.L.4
-
30
-
-
0034829463
-
Molecular dynamics simulations of the mononuclear zinc-β-lactamase from Bacillus cereus
-
Suarez D., Merz K.M. Molecular dynamics simulations of the mononuclear zinc-β-lactamase from Bacillus cereus. J. Am. Chem. Soc. 123:2001;3759-3770.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 3759-3770
-
-
Suarez, D.1
Merz, K.M.2
-
32
-
-
0028815118
-
Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion
-
Ryde U. Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion. Proteins Struct. Funct. Genet. 21:1995;40-56.
-
(1995)
Proteins Struct. Funct. Genet.
, vol.21
, pp. 40-56
-
-
Ryde, U.1
-
33
-
-
0025158237
-
A new force field for modeling metalloproteins
-
Vedani A., Huhta D.W. A new force field for modeling metalloproteins. J. Am. Chem. Soc. 112:1990;4759-4767.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 4759-4767
-
-
Vedani, A.1
Huhta, D.W.2
-
34
-
-
0029115487
-
Zinc binding in proteins and solution: A simple but accurate nonbonded representation
-
Stote R.H., Karplus M. Zinc binding in proteins and solution: a simple but accurate nonbonded representation. Proteins Struct. Funct. Genet. 23:1995;12-23.
-
(1995)
Proteins Struct. Funct. Genet.
, vol.23
, pp. 12-23
-
-
Stote, R.H.1
Karplus, M.2
-
35
-
-
0000768311
-
Zinc's exclusive tetrahedral coordination governed by its electronic structure
-
Roe R.R., Pang Y.P. Zinc's exclusive tetrahedral coordination governed by its electronic structure. J. Mol. Model. 5:1999;134-140.
-
(1999)
J. Mol. Model
, vol.5
, pp. 134-140
-
-
Roe, R.R.1
Pang, Y.P.2
-
36
-
-
0000510540
-
Novel zinc protein molecular dynamics simulations: Steps towards antiangiogenesis for cancer treatment
-
Pang Y.P. Novel zinc protein molecular dynamics simulations: steps towards antiangiogenesis for cancer treatment. J. Mol. Model. 5:1999;196-202.
-
(1999)
J. Mol. Model
, vol.5
, pp. 196-202
-
-
Pang, Y.P.1
-
37
-
-
0033535565
-
Binding preferences of hydroxamate inhibitors of the matrix metalloproteinase human fibroblast collagenase
-
Toba S., Damodaran K.V., Merz K.M. Binding preferences of hydroxamate inhibitors of the matrix metalloproteinase human fibroblast collagenase. J. Med. Chem. 42:1999;1225-1234.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 1225-1234
-
-
Toba, S.1
Damodaran, K.V.2
Merz, K.M.3
-
38
-
-
0035819590
-
Mobility of the active site bound paraoxon and sarin in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation
-
Koca J., Zhan C.-G., Rittenhouse R.C., Ornstein R.L. Mobility of the active site bound paraoxon and sarin in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation. J. Am. Chem. Soc. 123:2001;817-826.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 817-826
-
-
Koca, J.1
Zhan, C.-G.2
Rittenhouse, R.C.3
Ornstein, R.L.4
-
39
-
-
0034597622
-
Calculations and prediction of binding free energies for matrix metalloproeinases
-
It reports for the first time calculations on the inhibitor binding entropy, through a single-point normal mode approach. This is an inexpensive methodology to rank relative binding constants of potential drug molecules.
-
Donini O.A.T., Kollman P.A. Calculations and prediction of binding free energies for matrix metalloproeinases. J. Med. Chem. 43:2000;4180-4188 It reports for the first time calculations on the inhibitor binding entropy, through a single-point normal mode approach. This is an inexpensive methodology to rank relative binding constants of potential drug molecules.
-
(2000)
J. Med. Chem.
, vol.43
, pp. 4180-4188
-
-
Donini, O.A.T.1
Kollman, P.A.2
-
40
-
-
84986492477
-
Atomic charges derived from semiempirical methods
-
Besler B.H., Merz K.M., Kollman P.A. Atomic charges derived from semiempirical methods. J. Comp. Chem. 11:1990;431-439.
-
(1990)
J. Comp. Chem.
, vol.11
, pp. 431-439
-
-
Besler, B.H.1
Merz, K.M.2
Kollman, P.A.3
-
41
-
-
0000730887
-
Application of the RESP methodology in the parameterization of organic solvents
-
Fox T., Kollman P.A. Application of the RESP methodology in the parameterization of organic solvents. J. Phys. Chem. B. 102:1998;8070-8079.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 8070-8079
-
-
Fox, T.1
Kollman, P.A.2
-
42
-
-
0345491105
-
Development of the Colle-Salvetti correlation-energy formula into a functional of electron density
-
Lee C., Yang W., Parr R.G. Development of the Colle-Salvetti correlation-energy formula into a functional of electron density. Phys. Rev. B. 37:1988;785-789.
-
(1988)
Phys. Rev. B
, vol.37
, pp. 785-789
-
-
Lee, C.1
Yang, W.2
Parr, R.G.3
-
43
-
-
0036536998
-
Theoretical and computational models of ion channels
-
Roux B. Theoretical and computational models of ion channels. Curr. Opin. Struct. Biol. 12:2002;182-189.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 182-189
-
-
Roux, B.1
-
44
-
-
0037071785
-
Potassium permeation through the KcsA channel: A density functional study
-
Guidoni L., Carloni P. Potassium permeation through the KcsA channel: a density functional study. Biochim. Biophys. Acta. 1563:2002;1-6.
-
(2002)
Biochim. Biophys. Acta.
, vol.1563
, pp. 1-6
-
-
Guidoni, L.1
Carloni, P.2
-
45
-
-
0034669776
-
Molecular dynamics simulation of the β domain of metallothionein with a semi-empirical treatment of the metal core
-
Berweger C.D., Thiel W., Van Gunsteren W.F. Molecular dynamics simulation of the β domain of metallothionein with a semi-empirical treatment of the metal core. Proteins. 41:2000;299-315.
-
(2000)
Proteins
, vol.41
, pp. 299-315
-
-
Berweger, C.D.1
Thiel, W.2
Van Gunsteren, W.F.3
-
46
-
-
0033549110
-
A hybrid density functional theory/molecular mechanics study of nickel-iron hydrogenase: Investigation of the active site redox states
-
Amara P., Volbeda A., Fontecilla-Camps J.C., Field M.J. A hybrid density functional theory/molecular mechanics study of nickel-iron hydrogenase: investigation of the active site redox states. J. Am. Chem. Soc. 121:1999;4468-4477.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 4468-4477
-
-
Amara, P.1
Volbeda, A.2
Fontecilla-Camps, J.C.3
Field, M.J.4
-
47
-
-
0032876931
-
A molecular mechanics analysis of the active site of urease with a special emphasis on determining the binding conformations available to oxygen-bound urea
-
Csiki C., Zimmer M. A molecular mechanics analysis of the active site of urease with a special emphasis on determining the binding conformations available to oxygen-bound urea. J. Biomol. Struct. Dyn. 17:1999;121-131.
-
(1999)
J. Biomol. Struct. Dyn.
, vol.17
, pp. 121-131
-
-
Csiki, C.1
Zimmer, M.2
-
48
-
-
0025026406
-
Insights into the function of the zinc-hydroxide-Thr 199-Glu 106 hydrogen bonding network in carbonic anhydrase
-
Merz K.M. Jr. Insights into the function of the zinc-hydroxide-Thr 199-Glu 106 hydrogen bonding network in carbonic anhydrase. J. Mol. Biol. 214:1990;799.
-
(1990)
J. Mol. Biol.
, vol.214
, pp. 799
-
-
Merz K.M., Jr.1
-
49
-
-
0026035371
-
2 binding to human carbonic anhydrase II
-
2 binding to human carbonic anhydrase II. J. Am. Chem. Soc. 113:1991;406-411.
-
(1991)
J. Am. Chem. Soc.
, vol.113
, pp. 406-411
-
-
Merz K.M., Jr.1
-
50
-
-
0026661447
-
Molecular dynamics characterization of the active cavity of carboxypeptidase A and some of its inhibitor adducts
-
Banci L., Schroeder S., Kollman P.A. Molecular dynamics characterization of the active cavity of carboxypeptidase A and some of its inhibitor adducts. Proteins Struct. Funct. Genet. 13:1992;288-305.
-
(1992)
Proteins Struct. Funct. Genet
, vol.13
, pp. 288-305
-
-
Banci, L.1
Schroeder, S.2
Kollman, P.A.3
-
51
-
-
0027517866
-
Binding of cyanide, cyanate, and thiocyanate to human carbonic anhydrase II
-
Peng Z., Merz K.M. Jr., Banci L. Binding of cyanide, cyanate, and thiocyanate to human carbonic anhydrase II. Proteins. 17:1993;203-216.
-
(1993)
Proteins
, vol.17
, pp. 203-216
-
-
Peng, Z.1
Merz K.M., Jr.2
Banci, L.3
-
52
-
-
0033577309
-
Solvent dynamics and mechanism of proton transfer in human carbonic anhydrase II
-
Toba S., Colombo G., Merz K.M. Solvent dynamics and mechanism of proton transfer in human carbonic anhydrase II. J. Am. Chem. Soc. 121:1999;2290-2302.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 2290-2302
-
-
Toba, S.1
Colombo, G.2
Merz, K.M.3
-
54
-
-
0004152433
-
-
Chichester, UK: Wiley
-
Anon.: Handbook of Metalloproteins. Chichester, UK: Wiley; 2001:1-1248.
-
(2001)
Handbook of Metalloproteins
, pp. 1-1248
-
-
-
55
-
-
0037188355
-
Insights into the structure and dynamics of the dinuclear zinc-β-lactamase site from Bacteroides fragilis
-
This paper reports an example of QM/MM calculations for the characterization of the reaction pathway of the β-lactamase enzyme.
-
Suarez D., Brothers E.N., Merz K.M. Insights into the structure and dynamics of the dinuclear zinc-β-lactamase site from Bacteroides fragilis. Biochemistry. 41:2002;6615-6630 This paper reports an example of QM/MM calculations for the characterization of the reaction pathway of the β-lactamase enzyme.
-
(2002)
Biochemistry
, vol.41
, pp. 6615-6630
-
-
Suarez, D.1
Brothers, E.N.2
Merz, K.M.3
-
56
-
-
0037025301
-
Substrate-activated zinc binding of metallo-β-lactamases
-
Wommer S., Rival S., Heinz U., Galleni M., Frère J.-M., Franceschini N., Amicosante G., Rasmussen B., Bauer R., Adolph H.-W. Substrate-activated zinc binding of metallo-β-lactamases. J. Biol. Chem. 277:2002;24142-24147.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 24142-24147
-
-
Wommer, S.1
Rival, S.2
Heinz, U.3
Galleni, M.4
Frère, J.-M.5
Franceschini, N.6
Amicosante, G.7
Rasmussen, B.8
Bauer, R.9
Adolph, H.-W.10
-
58
-
-
0035854280
-
2+
-
2+. J. Mol. Biol. 310:2001;659-672.
-
(2001)
J. Mol. Biol.
, vol.310
, pp. 659-672
-
-
Bombarda, E.1
Morellet, N.2
Cherradi, H.3
Spiess, B.4
Bouaziz, S.5
Grell, E.6
Roques, B.P.7
Mély, Y.8
-
59
-
-
0034613034
-
NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex
-
Tsui V., Radhakrishnan I., Wright P.E., Case D.A. NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex. J. Mol. Biol. 302:2000;1101-1117.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 1101-1117
-
-
Tsui, V.1
Radhakrishnan, I.2
Wright, P.E.3
Case, D.A.4
-
60
-
-
0035822178
-
Binding affinities for a series of selective inhibitors of gelatinase-A using molecular dynamics with a linear interaction energy approach
-
Hou T.J., Zhang W., Xu X.J. Binding affinities for a series of selective inhibitors of gelatinase-A using molecular dynamics with a linear interaction energy approach. J. Phys. Chem. B. 105:2001;5304-5315.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 5304-5315
-
-
Hou, T.J.1
Zhang, W.2
Xu, X.J.3
-
61
-
-
0343416136
-
Molecular dynamics simulation of metallothionein-drug complexes
-
Szilágyi Z., Fenselau C. Molecular dynamics simulation of metallothionein-drug complexes. Drug Metab. Dispos. 28:2000;174-179.
-
(2000)
Drug Metab. Dispos.
, vol.28
, pp. 174-179
-
-
Szilágyi, Z.1
Fenselau, C.2
-
62
-
-
0035798652
-
Characterization of the binding interface between the copper chaperone Atx1 and the first cytosolic domain of Ccc2 ATPase
-
Arnesano F., Banci L., Bertini I., Cantini F., Ciofi-Baffoni S., Huffman D.L., O'Halloran T.V. Characterization of the binding interface between the copper chaperone Atx1 and the first cytosolic domain of Ccc2 ATPase. J. Biol. Chem. 276:2001;41365-41376.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 41365-41376
-
-
Arnesano, F.1
Banci, L.2
Bertini, I.3
Cantini, F.4
Ciofi-Baffoni, S.5
Huffman, D.L.6
O'Halloran, T.V.7
-
63
-
-
0037066740
-
Molecular dynamics characterization of the C2 domain of protein kinase Cβ
-
Banci L., Cavallaro G., Kheifets V., Mochly-Rosen D. Molecular dynamics characterization of the C2 domain of protein kinase Cβ J. Biol. Chem. 277:2002;12988-12997.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 12988-12997
-
-
Banci, L.1
Cavallaro, G.2
Kheifets, V.3
Mochly-Rosen, D.4
-
64
-
-
0034480099
-
Ras upon GAP-334 complexation as probed by ESEEM spectroscopy and molecular-dynamics simulation
-
This paper constitutes a nice example of the combination of experimentally derived constraints on a metal centre with MD simulations to obtain a reliable solution structural model.
-
Ras upon GAP-334 complexation as probed by ESEEM spectroscopy and molecular-dynamics simulation. Structure. 8:2000;1279-1287 This paper constitutes a nice example of the combination of experimentally derived constraints on a metal centre with MD simulations to obtain a reliable solution structural model.
-
(2000)
Structure
, vol.8
, pp. 1279-1287
-
-
Farrar, C.T.1
Ma, J.2
Singel, D.3
Halides, C.J.4
-
65
-
-
0000649135
-
PSEUDODYANA for NMR structure calculation of paramagnetic metalloproteins using torsion angle molecular dynamics
-
Banci L., Bertini I., Cremonini M.A., Gori Savellini G., Luchinat C., Wüthrich K., Güntert P. PSEUDODYANA for NMR structure calculation of paramagnetic metalloproteins using torsion angle molecular dynamics. J. Biomol. NMR. 12:1998;553-557.
-
(1998)
J. Biomol. NMR
, vol.12
, pp. 553-557
-
-
Banci, L.1
Bertini, I.2
Cremonini, M.A.3
Gori Savellini, G.4
Luchinat, C.5
Wüthrich, K.6
Güntert, P.7
-
66
-
-
0030954693
-
The pseudocontact shifts as constraints for energy minimization and molecular dynamic calculations on solution structures of paramagnetic metalloproteins
-
Banci L., Bertini I., Gori Savellini G., Romagnoli A., Turano P., Cremonini M.A., Luchinat C., Gray H.B. The pseudocontact shifts as constraints for energy minimization and molecular dynamic calculations on solution structures of paramagnetic metalloproteins. Proteins Struct. Funct. Genet. 29:1997;68-76.
-
(1997)
Proteins Struct. Funct. Genet.
, vol.29
, pp. 68-76
-
-
Banci, L.1
Bertini, I.2
Gori Savellini, G.3
Romagnoli, A.4
Turano, P.5
Cremonini, M.A.6
Luchinat, C.7
Gray, H.B.8
-
67
-
-
0036838489
-
Studies of metal binding reactions in metallothioneins by spectroscopic, molecular biology, and molecular modeling techniques
-
Chan J., Huang Z., Merrifield M.E., Salgado M.T., Stillman M.J. Studies of metal binding reactions in metallothioneins by spectroscopic, molecular biology, and molecular modeling techniques. Coord. Chem. Rev. 233-234:2002;319-339.
-
(2002)
Coord. Chem. Rev.
, vol.233-234
, pp. 319-339
-
-
Chan, J.1
Huang, Z.2
Merrifield, M.E.3
Salgado, M.T.4
Stillman, M.J.5
-
69
-
-
0035371926
-
Proton transfer in Azotobacter vinelandii ferredoxin I: Entatic Lys84 operates as elastic counterbalance for the proton-carrying Asp15
-
Cherepanov D.A., Mulkidjanian A.Y. Proton transfer in Azotobacter vinelandii ferredoxin I: entatic Lys84 operates as elastic counterbalance for the proton-carrying Asp15. Biochim. Biophys. Acta. 1505:2001;179-184.
-
(2001)
Biochim. Biophys. Acta.
, vol.1505
, pp. 179-184
-
-
Cherepanov, D.A.1
Mulkidjanian, A.Y.2
-
70
-
-
0034659779
-
Atomically defined mechanism for proton transfer to a buried redox centre in a protein
-
The proton transfer process coupled to a single long-range electron-transfer process is characterized in ferredoxin I, through a combination of experimental and theoretical methods.
-
Chen K., Hirst J., Camba R., Bonagura C.A., Stout C.D., Burgess B.A., Armstrong F.A. Atomically defined mechanism for proton transfer to a buried redox centre in a protein. Nature. 405:2000;814-817 The proton transfer process coupled to a single long-range electron-transfer process is characterized in ferredoxin I, through a combination of experimental and theoretical methods.
-
(2000)
Nature
, vol.405
, pp. 814-817
-
-
Chen, K.1
Hirst, J.2
Camba, R.3
Bonagura, C.A.4
Stout, C.D.5
Burgess, B.A.6
Armstrong, F.A.7
-
72
-
-
0018791973
-
Dynamics of ligand binding to heme proteins
-
Case D.A., Karplus M. Dynamics of ligand binding to heme proteins. J. Mol. Biol. 132:1979;343-368.
-
(1979)
J. Mol. Biol.
, vol.132
, pp. 343-368
-
-
Case, D.A.1
Karplus, M.2
-
73
-
-
0037054838
-
NO rebinding to myoglobin: A reactive molecular dynamics study
-
Meuwly M., Becker O.M., Stote R., Karplus M. NO rebinding to myoglobin: a reactive molecular dynamics study. Biophys. Chem. 98:2002;183-207.
-
(2002)
Biophys. Chem.
, vol.98
, pp. 183-207
-
-
Meuwly, M.1
Becker, O.M.2
Stote, R.3
Karplus, M.4
-
74
-
-
0034951055
-
Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: A QM/MM density functional study
-
Rovira C., Schulze B., Eichinger M., Evanseck J.D., Parrinello M. Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study. Biophys. J. 81:2001;435-445.
-
(2001)
Biophys. J.
, vol.81
, pp. 435-445
-
-
Rovira, C.1
Schulze, B.2
Eichinger, M.3
Evanseck, J.D.4
Parrinello, M.5
-
75
-
-
0035821590
-
Metabolism of sirolimus and its derivative everolimus by cytochrome P450 3A4: Insights from docking, molecular dynamics, and quantum chemical calculations
-
Kuhn B., Jacobsen W., Christians U., Benet L.Z., Kollman P.A. Metabolism of sirolimus and its derivative everolimus by cytochrome P450 3A4: insights from docking, molecular dynamics, and quantum chemical calculations. J. Med. Chem. 44:2001;2027-2034.
-
(2001)
J. Med. Chem.
, vol.44
, pp. 2027-2034
-
-
Kuhn, B.1
Jacobsen, W.2
Christians, U.3
Benet, L.Z.4
Kollman, P.A.5
-
76
-
-
0035802360
-
Theoretical study of the mechanisms of substrate recognition by catalase
-
In this paper, the use of a variety of theoretical methods, mainly based on a classical approach, lead the authors to rationalize the catalytic properties of catalase.
-
Kalko S.G., Gelpi J.L., Fita I., Orozco M. Theoretical study of the mechanisms of substrate recognition by catalase. J. Am. Chem. Soc. 123:2001;9665-9672 In this paper, the use of a variety of theoretical methods, mainly based on a classical approach, lead the authors to rationalize the catalytic properties of catalase.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 9665-9672
-
-
Kalko, S.G.1
Gelpi, J.L.2
Fita, I.3
Orozco, M.4
-
77
-
-
0035204346
-
Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f
-
De Rienzo F., Gabdoulline R.R., Menziani C.M., De Benedetti P.G., Wade R.C. Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f. Biophys. J. 81:2001;3090-3104.
-
(2001)
Biophys. J.
, vol.81
, pp. 3090-3104
-
-
De Rienzo, F.1
Gabdoulline, R.R.2
Menziani, C.M.3
De Benedetti, P.G.4
Wade, R.C.5
-
78
-
-
0039591353
-
Side-chain interactions in the plastocyanin-cytochrome f complex
-
Ejdeback M., Bergkvist A., Karlsson B.G., Ubbink M. Side-chain interactions in the plastocyanin-cytochrome f complex. Biochemistry. 39:2000;5022-5027.
-
(2000)
Biochemistry
, vol.39
, pp. 5022-5027
-
-
Ejdeback, M.1
Bergkvist, A.2
Karlsson, B.G.3
Ubbink, M.4
-
79
-
-
0035869698
-
Concerted motions in copper plastocyanin and azurin: An essential dynamics study
-
Arcangeli C., Bizzarri A.R., Cannistraro S. Concerted motions in copper plastocyanin and azurin: an essential dynamics study. Biophys. Chem. 90:2001;45-56.
-
(2001)
Biophys. Chem.
, vol.90
, pp. 45-56
-
-
Arcangeli, C.1
Bizzarri, A.R.2
Cannistraro, S.3
-
80
-
-
0033995767
-
Molecular dynamics simulation of solvated azurin: Correlation between surface solvent accessibility and water residence times
-
Luise A., Falconi M., Desideri A. Molecular dynamics simulation of solvated azurin: correlation between surface solvent accessibility and water residence times. Proteins. 39:2000;56-67.
-
(2000)
Proteins
, vol.39
, pp. 56-67
-
-
Luise, A.1
Falconi, M.2
Desideri, A.3
-
81
-
-
0034622546
-
Backbone dynamics of human Cu, Zn superoxide dismustase and of its monomeric F50/EG51E/E133Q mutant: The influence of dimerization on mobility and function
-
Banci L., Bertini I., Cramaro F., Del Conte R., Rosato A., Viezzoli M.S. Backbone dynamics of human Cu, Zn superoxide dismustase and of its monomeric F50/EG51E/E133Q mutant: the influence of dimerization on mobility and function. Biochemistry. 39:2000;9108-9118.
-
(2000)
Biochemistry
, vol.39
, pp. 9108-9118
-
-
Banci, L.1
Bertini, I.2
Cramaro, F.3
Del Conte, R.4
Rosato, A.5
Viezzoli, M.S.6
-
82
-
-
0026675574
-
Molecular dynamics studies on superoxide dismutase and its mutants: The structural and functional role of Arg 143
-
Banci L., Carloni P., La Penna G., Orioli P.L. Molecular dynamics studies on superoxide dismutase and its mutants: the structural and functional role of Arg 143. J. Am. Chem. Soc. 114:1992;6994-7001.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 6994-7001
-
-
Banci, L.1
Carloni, P.2
La Penna, G.3
Orioli, P.L.4
-
83
-
-
0028220301
-
Molecular dynamics studies on mutants of Cu,Zn superoxide dismutase: The functional role of charged residues in the electrostatic loop VII
-
Banci L., Carloni P., Orioli P.L. Molecular dynamics studies on mutants of Cu,Zn superoxide dismutase: the functional role of charged residues in the electrostatic loop VII. Proteins. 18:1994;216-230.
-
(1994)
Proteins
, vol.18
, pp. 216-230
-
-
Banci, L.1
Carloni, P.2
Orioli, P.L.3
-
84
-
-
0035016928
-
Dynamics-function correlation in Cu,Zn superoxide dismutase: A spectroscopic and molecular dynamics simulation study
-
Falconi M., Stroppolo M.E., Cioni P., Strambini G., Sergi A., Ferrario M., Desideri A. Dynamics-function correlation in Cu,Zn superoxide dismutase: a spectroscopic and molecular dynamics simulation study. Biophys. J. 80:2001;2556-2567.
-
(2001)
Biophys. J.
, vol.80
, pp. 2556-2567
-
-
Falconi, M.1
Stroppolo, M.E.2
Cioni, P.3
Strambini, G.4
Sergi, A.5
Ferrario, M.6
Desideri, A.7
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