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51

Exploring the origin of the ion selectivity of the KcsA potassium channel

Anton Burykin, Mitsunori Kato, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 1.01 MB

english, 2003

52

Why does the Ras switch “break” by oncogenic mutations?

Avital Shurki, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 595 KB

english, 2004

53

Exploring the role of large conformational changes in the fidelity of DNA polymerase β

Yun Xiang, Myron F. Goodman, William A. Beard, Samuel H. Wilson, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 622 KB

english, 2008

54

Effective approach for calculations of absolute stability of proteins using focused dielectric constants

Spyridon Vicatos, Maite Roca, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 459 KB

english, 2009

55

A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases

Robert Rucker, Peter Oelschlaeger, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 388 KB

english, 2010

56

Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models

Benjamin M. Messer, Maite Roca, Zhen T. Chu, Spyridon Vicatos, Alexandra Vardi Kilshtain, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 797 KB

english, 2010

57

A comprehensive examination of the contributions to the binding entropy of protein–ligand complexes

Nidhi Singh, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 413 KB

english, 2010

58

Absolute binding free energy calculations: On the accuracy of computational scoring of protein–ligand interactions

Nidhi Singh, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 722 KB

english, 2010

59

Simulating electrostatic energies in proteins: Perspectives and some recent studies of pKas, redox, and other crucial functional properties

Arieh Warshel, Anatoly Dryga

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 543 KB

english, 2011

60

Prechemistry versus preorganization in DNA replication fidelity

B. Ram Prasad, Arieh Warshel

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 2.56 MB

english, 2011

61

Microscopic simulation of quantum dynamics and nuclear tunneling in bacterial reaction centers

Zhen Tao Chu, Arieh Warshel, William W. Parson

Journal:

Photosynthesis Research

Year:

1984

Language:

english

File:

PDF, 531 KB

english, 1984

62

Calculations of the electrostatic free energy contributions to the binding free energy of sulfonamides to carbonic anhydrase

Jeffry D. Madura, Yasushi Nakajima, Rodney M. Hamilton, Andrzej Wierzbicki, Arieh Warshel

Journal:

Structural Chemistry

Year:

1996

Language:

english

File:

PDF, 514 KB

english, 1996

63

Perspective on “The energetics of enzymatic reactions”

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2000

Language:

english

File:

PDF, 70 KB

english, 2000

64

Simulating large nuclear quantum mechanical corrections in hydrogen atom transfer reactions in metalloenzymes

MatsH.M. Olsson, PerE.M. Siegbahn, Arieh Warshel

Journal:

JBIC Journal of Biological Inorganic Chemistry

Year:

2004

Language:

english

File:

PDF, 733 KB

english, 2004

65

Bicycle-pedal model for the first step in the vision process

Journal:

Year:

1976

File:

PDF, 596 KB

1976

66

What about protein polarity?

Journal:

Year:

1987

File:

PDF, 287 KB

1987

67

Why ion pair reversal by protein engineering is unlikely to succeed

Hwang, Jenn-Kang, Warshel, Arieh

Journal:

Year:

1988

File:

PDF, 484 KB

1988

68

Substrate-assisted catalysis as a mechanism for GTP hydrolysis of p21ras and other GTP-binding proteins

Schweins, Thomas, Geyer, Matthias, Scheffzek, Klaus, Warshel, Arieh, Kalbitzer, Hans Robert, Wittinghofer, Alfred

Journal:

Natural Structural Biology

Year:

1995

File:

PDF, 830 KB

1995

69

Oscillations of the energy gap for the initial electron-transfer step in bacterial reaction centers

William W. Parson, Zhen Tao Chu, Arieh Warshel

Journal:

Photosynthesis Research

Year:

1998

Language:

english

File:

PDF, 205 KB

english, 1998

70

DNA Polymerase β Fidelity: Halomethylene-Modified Leaving Groups in Pre-Steady-State Kinetic Analysis Reveal Differences at the Chemical Transition State†

Sucato, Christopher A., Upton, Thomas G., Kashemirov, Boris A., Osuna, Jorge, Oertell, Keriann, Beard, William A., Wilson, Samuel H., Florián, Jan, Warshel, Arieh, McKenna, Charles E.

Journal:

Year:

2008

Language:

english

File:

PDF, 236 KB

english, 2008

71

Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron-transfer and proton-transfer reactions

Journal:

Journal of Physical Chemistry

Year:

1982

Language:

english

File:

PDF, 889 KB

english, 1982

72

Frozen Density Functional Free Energy Simulations of Redox Proteins: Computational Studies of the Reduction Potential of Plastocyanin and Rusticyanin

Olsson, Mats H. M., Hong, Gongyi, Warshel, Arieh

Journal:

Journal of the American Chemical Society

Year:

2003

Language:

english

File:

PDF, 532 KB

english, 2003

73

Computer Simulation of the Chemical Catalysis of DNA Polymerases: Discriminating between Alternative Nucleotide Insertion Mechanisms for T7 DNA Polymerase

Florián, Jan, Goodman, Myron F., Warshel, Arieh

Journal:

Journal of the American Chemical Society

Year:

2003

Language:

english

File:

PDF, 341 KB

english, 2003

74

Molecular Dynamics Simulations of Biological Reactions

Journal:

Accounts of Chemical Research

Year:

2002

Language:

english

File:

PDF, 476 KB

english, 2002

75

Simulations of the Large Kinetic Isotope Effect and the Temperature Dependence of the Hydrogen Atom Transfer in Lipoxygenase

Olsson, Mats H. M., Siegbahn, Per E. M., Warshel, Arieh

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 205 KB

english, 2004

76

The empirical valence bond as an effective strategy for computer-aided enzyme design

Alexandra Vardi-Kilshtain, Maite Roca, Arieh Warshel

Journal:

Biotechnology Journal

Year:

2009

Language:

english

File:

PDF, 199 KB

english, 2009

77

Computer simulations of enzymatic reactions

Journal:

Current Biology

Year:

1992

Language:

english

File:

PDF, 127 KB

english, 1992

78

Computer simulations of proton transfer in cytochrome c oxidase and nitric oxide reductase

Andrei Pisliakov, Yuji Sugita, Arieh Warshel

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2010

Language:

english

File:

PDF, 80 KB

english, 2010

79

Proton-transport mechanisms in cytochrome c oxidase revealed by studies of kinetic isotope effects

Ann-Louise Johansson, Suman Chakrabarty, Catrine L. Berthold, Martin Högbom, Arieh Warshel, Peter Brzezinski

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2011

Language:

english

File:

PDF, 1.02 MB

english, 2011

80

Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects

Suman Chakrabarty, Ida Namslauer, Peter Brzezinski, Arieh Warshel

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

2011

Language:

english

File:

PDF, 1.46 MB

english, 2011

81

CONVERSION OF LIGHT ENERGY TO ELECTROSTATIC ENERGY IN THE PROTON PUMP OF HALOBACTERIUM HALOBIUM

Journal:

Photochemistry and Photobiology

Year:

1979

Language:

english

File:

PDF, 479 KB

english, 1979

82

Spectroscopic properties of photosynthetic reaction centers. 2. Application of the theory to Rhodopseudomonas viridis

Parson, William W., Warshel, Arieh

Journal:

Journal of the American Chemical Society

Year:

1987

Language:

english

File:

PDF, 1.49 MB

english, 1987

83

Spectroscopic properties of photosynthetic reaction centers. 1. Theory

Warshel, Arieh, Parson, William W.

Journal:

Journal of the American Chemical Society

Year:

1987

Language:

english

File:

PDF, 1.27 MB

english, 1987

84

Origin of the Catalytic Power of Acetylcholinesterase: Computer Simulation Studies

Fuxreiter, Monika, Warshel, Arieh

Journal:

Journal of the American Chemical Society

Year:

1998

Language:

english

File:

PDF, 156 KB

english, 1998

85

Exploring, Refining, and Validating the Paradynamics QM/MM Sampling

Plotnikov, Nikolay V., Warshel, Arieh

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 729 KB

english, 2012

86

Microscopic simulations of macroscopic dielectric constants of solvated proteins

King, Gregory, Lee, Frederick S., Warshel, Arieh

Journal:

The Journal of Chemical Physics

Year:

1991

Language:

english

File:

PDF, 1.17 MB

english, 1991

87

Calculations of electrostatic interactions in biological systems and in solutions

Warshel, Arieh, Russell, Stephen T.

Journal:

Quarterly Reviews of Biophysics

Year:

1984

Language:

english

File:

PDF, 6.08 MB

english, 1984

88

Electrostatic control of charge separation in bacterial photosynthesis

William W. Parson, Zhen-Tao Chu, Arieh Warshel

Journal:

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Year:

1990

Language:

english

File:

PDF, 2.12 MB

english, 1990

89

Computer simulation of the initial proton transfer step in human carbonic anhydrase I

Johan Åqvist, Arieh Warshel

Journal:

Journal of Molecular Biology

Year:

1992

Language:

english

File:

PDF, 2.13 MB

english, 1992

90

Coarse grained model for exploring voltage dependent ion channels

Anatoly Dryga, Suman Chakrabarty, Spyridon Vicatos, Arieh Warshel

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2012

Language:

english

File:

PDF, 1.38 MB

english, 2012

91

On the origin of the electrostatic barrier for proton transport in aquaporin

Anton Burykin, Arieh Warshel

Journal:

Year:

2004

Language:

english

File:

PDF, 246 KB

english, 2004

92

Simulating redox coupled proton transfer in cytochrome c oxidase: Looking for the proton bottleneck

Mats H.M. Olsson, Pankaz K. Sharma, Arieh Warshel

Journal:

Year:

2005

Language:

english

File:

PDF, 425 KB

english, 2005

93

Magnesium-cationic Dummy Atom Molecules Enhance Representation of DNA Polymerase β in Molecular Dynamics Simulations: Improved Accuracy in Studies of Structural Features and Mutational Effects

Peter Oelschlaeger, Marco Klahn, William A. Beard, Samuel H. Wilson, Arieh Warshel

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1.18 MB

english, 2007

94

Electrostatic effects in macromolecules: fundamental concepts and practical modeling

Arieh Warshel, Arno Papazyan

Journal:

Current Opinion in Structural Biology

Year:

1998

Language:

english

File:

PDF, 766 KB

english, 1998

95

On the Interpretation of the Observed Linear Free Energy Relationship in Phosphate Hydrolysis: A Thorough Computational Study of Phosphate Diester Hydrolysis in Solution †

Rosta, Edina, Kamerlin, Shina C. L., Warshel, Arieh

Journal:

Year:

2008

Language:

english

File:

PDF, 1.35 MB

english, 2008

96

Electrostatic basis of structure-function correlation in proteins

Journal:

Accounts of Chemical Research

Year:

1981

Language:

english

File:

PDF, 1.45 MB

english, 1981

97

Phosphate Ester Hydrolysis in Aqueous Solution: Associative versus Dissociative Mechanisms

Florián, Jan, Warshel, Arieh

Journal:

Journal of Physical Chemistry B

Year:

1998

Language:

english

File:

PDF, 653 KB

english, 1998

98

Solute Solvent Dynamics and Energetics in Enzyme Catalysis: The S N 2 Reaction of Dehalogenase as a General Benchmark

Olsson, Mats H. M., Warshel, Arieh

Journal:

Journal of the American Chemical Society

Year:

2004

Language:

english

File:

PDF, 377 KB

english, 2004

99

Electrostatic Contributions to Binding of Transition State Analogues Can Be Very Different from the Corresponding Contributions to Catalysis: Phenolates Binding to the Oxyanion Hole of Ketosteroid Isomerase †

Warshel, Arieh, Sharma, Pankaz K., Chu, Zhen T., Åqvist, Johan

Journal:

Year:

2007

Language:

english

File:

PDF, 253 KB

english, 2007

100

Calculations of Activation Entropies of Chemical Reactions in Solution

Strajbl, Marek, Sham, Yuk Y., Villà, Jordi, Chu, Z.-T., Warshel, Arieh

Journal:

Journal of Physical Chemistry B

Year:

2000

Language:

english

File:

PDF, 93 KB

english, 2000

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