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51

Exchange frequency in replica exchange molecular dynamics

Sindhikara, Daniel, Meng, Yilin, Roitberg, Adrian E.

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 1.34 MB

english, 2008

52

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

Simmerling, Carlos, Strockbine, Bentley, Roitberg, Adrian E.

Journal:

Journal of the American Chemical Society

Year:

2002

Language:

english

File:

PDF, 96 KB

english, 2002

53

Conformational disorder in energy transfer: beyond Förster theory

Nelson, Tammie, Fernandez-Alberti, Sebastian, Roitberg, Adrian E., Tretiak, Sergei

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 3.40 MB

english, 2013

54

Nonadiabatic excited-state molecular dynamics: Numerical tests of convergence and parameters

Nelson, Tammie, Fernandez-Alberti, Sebastian, Chernyak, Vladimir, Roitberg, Adrian E., Tretiak, Sergei

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 1.22 MB

english, 2012

55

Electronic Spectra of the Nanostar Dendrimer: Theory and Experiment †

Palma, Julio L., Atas, Evrim, Hardison, Lindsay, Marder, Todd B., Collings, Jonathan C., Beeby, Andrew, Melinger, Joseph S., Krause, Jeffrey L., Kleiman, Valeria D., Roitberg, Adrian E.

Journal:

The Journal of Physical Chemistry C

Year:

2010

Language:

english

File:

PDF, 3.46 MB

english, 2010

56

Unidirectional Energy Transfer in Conjugated Molecules: The Crucial Role of High-Frequency C≡C Bonds

Fernandez-Alberti, S., Kleiman, Valeria D., Tretiak, S., Roitberg, Adrian E.

Journal:

The Journal of Physical Chemistry Letters

Year:

2010

Language:

english

File:

PDF, 1.70 MB

english, 2010

57

Electronic Delocalization in Coordination Polymers Based on Bimetallic Carboxylates

Castro, María Ana, Roitberg, Adrián E., Cukiernik, Fabio D.

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 1.42 MB

english, 2013

58

Conjugated Polyelectrolyte Dendrimers: Aggregation, Photophysics, and Amplified Quenching

Feng, Fude, Lee, Seoung Ho, Cho, Sung Won, Kömürlü, Sevnur, McCarley, Tracy D., Roitberg, Adrian, Kleiman, Valeria D., Schanze, Kirk S.

Journal:

Year:

2012

Language:

english

File:

PDF, 2.92 MB

english, 2012

59

Solvent-induced symmetry breaking of nitrate ion in aqueous clusters: A quantum-classical simulation study

González Lebrero, Mariano C., Bikiel, Damián E., Elola, M. Dolores, Estrin, Darı́o A., Roitberg, Adrian E.

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 468 KB

english, 2002

60

Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations

Meng, Yilin, Sabri Dashti, Danial, Roitberg, Adrian E.

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 1.05 MB

english, 2011

61

Multiple-Steering QM−MM Calculation of the Free Energy Profile in Chorismate Mutase

Crespo, Alejandro, Martí, Marcelo A., Estrin, Darío A., Roitberg, Adrian E.

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 122 KB

english, 2005

62

Enzyme dynamics and catalysis in the mechanism of DNA polymerase

Adrian J. Mulholland, Adrian E. Roitberg, Iñaki Tuñón

Journal:

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

Year:

2012

Language:

english

File:

PDF, 187 KB

english, 2012

63

A Multiscale Treatment of Angeli’s Salt Decomposition

Torras, Juan, Seabra, Gustavo de M., Roitberg, Adrian E.

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 1.69 MB

english, 2009

64

p38γ Activation Triggers Dynamical Changes in Allosteric Docking Sites

Rodriguez Limardo, Ramiro G., Ferreiro, Dardo N., Roitberg, Adrián E., Marti, Marcelo A., Turjanski, Adrian G.

Journal:

Year:

2011

Language:

english

File:

PDF, 4.50 MB

english, 2011

65

Free-energy computations identify the mutations required to confer trans-sialidase activity into Trypanosoma rangeli sialidase

Pierdominici-Sottile, Gustavo, Palma, Juliana, Roitberg, Adrian E.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.41 MB

english, 2014

66

Photosensitization of Single-Crystal ZnO by a Conjugated Polyelectrolyte Designed to Avoid Aggregation

Zhu, Xuzhi, Nepomnyashchii, Alexander B., Roitberg, Adrian E., Parkinson, B. A., Schanze, Kirk S.

Journal:

The Journal of Physical Chemistry Letters

Year:

2013

Language:

english

File:

PDF, 1.76 MB

english, 2013

67

Kinetics and computational studies of ligand migration in nitrophorin 7 and its Δ1–3 mutant

Oliveira, Ana, Allegri, Alessandro, Bidon-Chanal, Axel, Knipp, Markus, Roitberg, Adrian E., Abbruzzetti, Stefania, Viappiani, Cristiano, Luque, F. Javier

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2013

Language:

english

File:

PDF, 1.21 MB

english, 2013

68

Molecular Wires: Extended Coupling and Disorder Effects

Kemp, Mathieu, Roitberg, Adrian, Mujica, Vladimiro, Wanta, Todd, Ratner, Mark A.

Journal:

Journal of Physical Chemistry

Year:

1996

Language:

english

File:

PDF, 548 KB

english, 1996

69

Proton Transfer Facilitated by Ligand Binding. An Energetic Analysis of the Catalytic Mechanism of Trypanosoma cruzi Trans-Sialidase

Pierdominici-Sottile, Gustavo, Roitberg, Adrian E.

Journal:

Year:

2011

Language:

english

File:

PDF, 2.57 MB

english, 2011

70

AM1 Specific Reaction Parameters for Reactions of Hydroxide Ion with Halomethanes in Complex Environments: Development and Testing

Liang, Shuai, Roitberg, Adrian E.

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 1.27 MB

english, 2013

71

Electronic Excited State Specific IR Spectra for Phenylene Ethynylene Dendrimer Building Blocks

Galindo, Johan F., Fernandez-Alberti, Sebastian, Roitberg, Adrian E.

Journal:

The Journal of Physical Chemistry C

Year:

2013

Language:

english

File:

PDF, 2.10 MB

english, 2013

72

Design of e-pharmacophore models using compound fragments for the trans-sialidase of Trypanosoma cruzi: Screening for novel inhibitor scaffolds

Miller, Bill R., Roitberg, Adrian E.

Journal:

Journal of Molecular Graphics and Modelling

Year:

2013

Language:

english

File:

PDF, 2.32 MB

english, 2013

73

Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation

Swails, Jason M., York, Darrin M., Roitberg, Adrian E.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 3.84 MB

english, 2014

74

Unraveling the Differences of the Hydrolytic Activity of Trypanosoma cruzi trans -Sialidase and Trypanosoma rangeli Sialidase: A Quantum Mechanics–Molecular Mechanics Modeling Study

Bueren-Calabuig, Juan A., Pierdominici-Sottile, Gustavo, Roitberg, Adrian E.

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 525 KB

english, 2014

75

Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package †

Seabra, Gustavo de M., Walker, Ross C., Elstner, Marcus, Case, David A., Roitberg, Adrian E.

Journal:

Journal of Physical Chemistry A

Year:

2007

Language:

english

File:

PDF, 410 KB

english, 2007

76

AM1 Parameters for the Prediction of 1 H and 13 C NMR Chemical Shifts in Proteins †

Williams, Duane E., Peters, Martin B., Wang, Bing, Roitberg, Adrian E., Merz, Kenneth M.

Journal:

Journal of Physical Chemistry A

Year:

2009

Language:

english

File:

PDF, 1.27 MB

english, 2009

77

Molecular Dynamics of Poly(benzylphenyl ether) Dendrimers: Effects of Backfolding on Förster Energy-Transfer Rates

Ortiz, Wilfredo, Roitberg, Adrian E., Krause, Jeffrey L.

Journal:

Journal of Physical Chemistry B

Year:

2004

Language:

english

File:

PDF, 242 KB

english, 2004

78

A Vibrational Eigenfunction of a Protein: Anharmonic Coupled-Mode Ground and Fundamental Excited States of BPTI

Roitberg, Adrian E., Gerber, R. Benny, Ratner, Mark A.

Journal:

Journal of Physical Chemistry B

Year:

1997

Language:

english

File:

PDF, 147 KB

english, 1997

79

Wide-Open Flaps Are Key to Urease Activity

Roberts, Benjamin P., Miller, Bill R., Roitberg, Adrian E., Merz, Kenneth M.

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 4.40 MB

english, 2012

80

An MD/QM Study of the Chorismate Mutase-Catalyzed Claisen Rearrangement Reaction

Worthington, Sharon E., Roitberg, Adrian E., Krauss, Morris

Journal:

Journal of Physical Chemistry B

Year:

2001

Language:

english

File:

PDF, 309 KB

english, 2001

81

The Electronic Spectrum of the Prephenate Dianion. An Experimental and Theoretical (MD/QM) Comparison

Roitberg, Adrian E., Worthington, Sharon E., Holden, Marcia J., Mayhew, Martin P., Krauss, Morris

Journal:

Journal of the American Chemical Society

Year:

2000

Language:

english

File:

PDF, 87 KB

english, 2000

82

Benzocycloarene hydroxylation by P450 biocatalysis

Mayhew, Martin P., Roitberg, Adrian E., Tewari, Yadu, Holden, Marcia J., Vanderah, David J., Vilker, Vincent L.

Journal:

New Journal of Chemistry

Year:

2002

Language:

english

File:

PDF, 242 KB

english, 2002

83

Theoretical and Experimental Studies of Diruthenium Tetracarboxylates Structure, Spectroscopy, and Electrochemistry

Castro, Maria Ana, Roitberg, Adrian E., Cukiernik, Fabio D.

Journal:

Inorganic Chemistry

Year:

2008

Language:

english

File:

PDF, 1.85 MB

english, 2008

84

Binding and Electron Transfer between Putidaredoxin and Cytochrome P450cam. Theory and Experiments

Roitberg, Adrian E., Holden, Marcia J., Mayhew, Martin P., Kurnikov, Igor V., Beratan, David N., Vilker, Vincent L.

Journal:

Journal of the American Chemical Society

Year:

1998

Language:

english

File:

PDF, 109 KB

english, 1998

85

pH-Dependent Mechanism of Nitric Oxide Release in Nitrophorins 2 and 4

Swails, Jason M., Meng, Yilin, Walker, F. Ann, Marti, Marcelo A., Estrin, Dario A., Roitberg, Adrian E.

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 1.87 MB

english, 2009

86

Constant pH Replica Exchange Molecular Dynamics in Biomolecules Using a Discrete Protonation Model

Meng, Yilin, Roitberg, Adrian E.

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 3.15 MB

english, 2010

87

Crown Complexation of Protonated Amino Acids: Influence on IRMPD Spectra

Stedwell, Corey N., Galindo, Johan F., Gulyuz, Kerim, Roitberg, Adrian E., Polfer, Nicolas C.

Journal:

Journal of Physical Chemistry A

Year:

2013

Language:

english

File:

PDF, 1.16 MB

english, 2013

88

Modulation of Catalytic Function by Differential Plasticity of the Active Site: Case Study of Trypanosoma cruzi trans -Sialidase and Trypanosoma rangeli Sialidase †

Demir, Özlem, Roitberg, Adrian E.

Journal:

Year:

2009

Language:

english

File:

PDF, 3.51 MB

english, 2009

89

A DFT-Based QM-MM Approach Designed for the Treatment of Large Molecular Systems: Application to Chorismate Mutase

Crespo, Alejandro, Scherlis, Damián A., Martí, Marcelo A., Ordejón, Pablo, Roitberg, Adrián E., Estrin, Darío A.

Journal:

Journal of Physical Chemistry B

Year:

2003

Language:

english

File:

PDF, 212 KB

english, 2003

90

Improving Efficiency in SMD Simulations Through a Hybrid Differential Relaxation Algorithm

Ramírez, Claudia L., Zeida, Ari, Jara, Gabriel E., Roitberg, Adrián E., Martí, Marcelo A.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 608 KB

english, 2014

91

Computational Studies of Ammonia Channel Function in Glutamine 5′-Phosphoribosylpyrophosphate Amidotransferase

Wang, Xiang S., Roitberg, Adrian E., Richards, Nigel G. J.

Journal:

Year:

2009

Language:

english

File:

PDF, 7.88 MB

english, 2009

92

Coupling of Replica Exchange Simulations to a Non-Boltzmann Structure Reservoir

Roitberg, Adrian E., Okur, Asim, Simmerling, Carlos

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 117 KB

english, 2007

93

Nonadiabatic Molecular Dynamics Simulations of the Energy Transfer between Building Blocks in a Phenylene Ethynylene Dendrimer †

Fernandez-Alberti, Sebastian, Kleiman, Valeria D., Tretiak, Sergei, Roitberg, Adrian E.

Journal:

Journal of Physical Chemistry A

Year:

2009

Language:

english

File:

PDF, 1.63 MB

english, 2009

94

Exchange Often and Properly in Replica Exchange Molecular Dynamics

Sindhikara, Daniel J., Emerson, Daniel J., Roitberg, Adrian E.

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 731 KB

english, 2010

95

Simulating Temperature Jumps for Protein Folding

Kim, Seonah, Roitberg, Adrian E.

Journal:

Journal of Physical Chemistry B

Year:

2008

Language:

english

File:

PDF, 388 KB

english, 2008

96

Apo and Nickel-Bound Forms of the Pyrococcus horikoshii Species of the Metalloregulatory Protein: NikR Characterized by Molecular Dynamics Simulations

Sindhikara, Daniel J., Roitberg, Adrian E., Merz, Kenneth M.

Journal:

Year:

2009

Language:

english

File:

PDF, 4.11 MB

english, 2009

97

Catalytic Mechanism of L,D-Transpeptidase 2 from Mycobacterium tuberculosis Described by a Computational Approach: Insights for the Design of New Antibiotics Drugs

Silva, José Rogério A., Roitberg, Adrian E., Alves, Cláudio Nahum

Journal:

Journal of Chemical Information and Modeling

Year:

2014

Language:

english

File:

PDF, 2.23 MB

english, 2014

98

Smaller and Faster: The 20-Residue Trp-Cage Protein Folds in 4 μs

Qiu, Linlin, Pabit, Suzette A., Roitberg, Adrian E., Hagen, Stephen J.

Journal:

Journal of the American Chemical Society

Year:

2002

Language:

english

File:

PDF, 68 KB

english, 2002

99

Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide

Bergonzo, Christina, Henriksen, Niel M., Roe, Daniel R., Swails, Jason M., Roitberg, Adrian E., Cheatham, Thomas E.

Journal:

Journal of Chemical Theory and Computation

Year:

2014

Language:

english

File:

PDF, 2.77 MB

english, 2014

100

Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules

Sindhikara, Daniel J., Kim, Seonah, Voter, Arthur F., Roitberg, Adrian E.

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 2.52 MB

english, 2009