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The “Hot-Solvent/Cold-Solute” Problem Revisited

Journal of chemical theory and computation, 2008-08, Vol.4 (8), p.1293-1306

2008

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The Infrared Spectra of the Retinal Chromophore in Bacteriorhodopsin Calculated by a DFT/MM Approach

The journal of physical chemistry. B, 2009-07, Vol.113 (30), p.10496-10508

2009

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Polarization Effects Stabilize Bacteriorhodopsin’s Chromophore Binding Pocket: A Molecular Dynamics Study

The journal of physical chemistry. B, 2009-07, Vol.113 (30), p.10483-10495

2009

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A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields

The Journal of chemical physics, 1999-06, Vol.110 (21), p.10452-10467

1999

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FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations

Journal of computational chemistry, 1997-11, Vol.18 (14), p.1729-1749

1997

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Generalized radial basis function networks for classification and novelty detection: self-organization of optimal Bayesian decision

Neural networks, 2000-12, Vol.13 (10), p.1075-1093

2000

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Vibrational spectra from atomic fluctuations in dynamics simulations. I. Theory, limitations, and a sample application

The Journal of chemical physics, 2004-12, Vol.121 (24), p.12233-12246

2004

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Vibrational spectra from atomic fluctuations in dynamics simulations. II. Solvent-induced frequency fluctuations at femtosecond time resolution

The Journal of chemical physics, 2004-12, Vol.121 (24), p.12247-12258

2004

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Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force

Science (American Association for the Advancement of Science), 1996-02, Vol.271 (5251), p.997-999

1996

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A Self-Organizing Network for Principal-Component Analysis

Europhysics letters, 1989-12, Vol.10 (7), p.693-698

1989

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IR Spectra of Phosphate Ions in Aqueous Solution: Predictions of a DFT/MM Approach Compared with Observations

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2004-07, Vol.108 (29), p.6186-6194

2004

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Ultrafast Spectroscopy Reveals Subnanosecond Peptide Conformational Dynamics and Validates Molecular Dynamics Simulation

Proceedings of the National Academy of Sciences - PNAS, 2002-06, Vol.99 (12), p.7998-8002

2002

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A fast multipole method combined with a reaction field for long-range electrostatics in molecular dynamics simulations: The effects of truncation on the properties of water

The Journal of chemical physics, 2003-06, Vol.118 (24), p.10847-10860

2003

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Infrared Spectrum of p-Benzoquinone in Water Obtained from a QM/MM Hybrid Molecular Dynamics Simulation

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2003-10, Vol.107 (41), p.8638-8647

2003

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Molecular Dynamics Simulations Indicate a Possible Role of Parallel β-Helices in Seeded Aggregation of Poly-Gln

Biophysical journal, 2005-04, Vol.88 (4), p.2442-2451

2005

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FBR: a robust method to determine the basis matrix of the Bravais lattice from oscillation images

Journal of applied crystallography, 2000-06, Vol.33 (3-2), p.958-963

2000

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Extracting Markov Models of Peptide Conformational Dynamics from Simulation Data

Journal of chemical theory and computation, 2005-07, Vol.1 (4), p.515-526

2005

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Angular resolution and range of dipole-dipole correlations in water

The Journal of chemical physics, 2004-03, Vol.120 (9), p.4393-4403

2004

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Systematic Identification of Antiprion Drugs by High-Throughput Screening Based on Scanning for Intensely Fluorescent Targets

Journal of Virology, 2005-06, Vol.79 (12), p.7785-7791

2005

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A revised MRCI-algorithm coupled to an effective valence-shell Hamiltonian. II. Application to the valence excitations of butadiene

The Journal of chemical physics, 2002-09, Vol.117 (10), p.4677-4683

2002

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Structural Instability of the Prion Protein upon M205S/R Mutations Revealed by Molecular Dynamics Simulations

Biophysical journal, 2006-06, Vol.90 (11), p.3908-3918

2006

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The low-lying electronic excitations in long polyenes: a PPP-MRD-Cl study

The Journal of chemical physics, 1986-12, Vol.85 (11), p.6602-6609

1986

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Deactivation of Rhodopsin in the Transition from the Signaling State Meta II to Meta III Involves a Thermal Isomerization of the Retinal Chromophore CN Double Bond

Biochemistry (Easton), 2003-08, Vol.42 (33), p.9863-9874

2003

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Structures and Vibrational Frequencies of the Quinones in Rb. sphaeroides Derived by a Combined Density Functional/Molecular Mechanics Approach

The journal of physical chemistry. B, 2003-01, Vol.107 (1), p.316-322

2003

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Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution

The Journal of chemical physics, 2004-01, Vol.120 (4), p.2056-2068

2004

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The “Hot-Solvent/Cold-Solute” Problem Revisited

The Infrared Spectra of the Retinal Chromophore in Bacteriorhodopsin Calculated by a DFT/MM Approach

Polarization Effects Stabilize Bacteriorhodopsin’s Chromophore Binding Pocket: A Molecular Dynamics Study

A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields

FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations

Generalized radial basis function networks for classification and novelty detection: self-organization of optimal Bayesian decision

Vibrational spectra from atomic fluctuations in dynamics simulations. I. Theory, limitations, and a sample application

Vibrational spectra from atomic fluctuations in dynamics simulations. II. Solvent-induced frequency fluctuations at femtosecond time resolution

Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force

A Self-Organizing Network for Principal-Component Analysis

IR Spectra of Phosphate Ions in Aqueous Solution: Predictions of a DFT/MM Approach Compared with Observations

Ultrafast Spectroscopy Reveals Subnanosecond Peptide Conformational Dynamics and Validates Molecular Dynamics Simulation

A fast multipole method combined with a reaction field for long-range electrostatics in molecular dynamics simulations: The effects of truncation on the properties of water

Infrared Spectrum of p-Benzoquinone in Water Obtained from a QM/MM Hybrid Molecular Dynamics Simulation

Molecular Dynamics Simulations Indicate a Possible Role of Parallel β-Helices in Seeded Aggregation of Poly-Gln

FBR: a robust method to determine the basis matrix of the Bravais lattice from oscillation images

Extracting Markov Models of Peptide Conformational Dynamics from Simulation Data

Angular resolution and range of dipole-dipole correlations in water

Systematic Identification of Antiprion Drugs by High-Throughput Screening Based on Scanning for Intensely Fluorescent Targets

A revised MRCI-algorithm coupled to an effective valence-shell Hamiltonian. II. Application to the valence excitations of butadiene

Structural Instability of the Prion Protein upon M205S/R Mutations Revealed by Molecular Dynamics Simulations

The low-lying electronic excitations in long polyenes: a PPP-MRD-Cl study

Deactivation of Rhodopsin in the Transition from the Signaling State Meta II to Meta III Involves a Thermal Isomerization of the Retinal Chromophore CN Double Bond

Structures and Vibrational Frequencies of the Quinones in Rb. sphaeroides Derived by a Combined Density Functional/Molecular Mechanics Approach

Continuum description of ionic and dielectric shielding for molecular-dynamics simulations of proteins in solution

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