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Recent Advances in Computational Models for the Study of Protein-Peptide Interactions

Advances in protein chemistry and structural biology, 2016, Vol.105, p.27-57

2016

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Enthalpy−Entropy and Cavity Decomposition of Alkane Hydration Free Energies: Numerical Results and Implications for Theories of Hydrophobic Solvation

The journal of physical chemistry. B, 2000-07, Vol.104 (26), p.6271-6285

2000

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Synthesis and biological assessment of 3,7-dihydroxytropolones

Organic & biomolecular chemistry, 2017-12, Vol.16 (1), p.62-69

2017

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AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling

Journal of computational chemistry, 2004-03, Vol.25 (4), p.479-499

2004

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Integrated Modeling Program, Applied Chemical Theory (IMPACT)

Journal of computational chemistry, 2005-12, Vol.26 (16), p.1752-1780

2005

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The absorption spectrum of the solvated electron in fluid helium by maximum entropy inversion of imaginary time correlation functions from path integral Monte Carlo simulations

The Journal of chemical physics, 1994-12, Vol.101 (11), p.9909-9918

1994

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On the calculation of dynamical properties of solvated electrons by maximum entropy analytic continuation of path integral Monte Carlo data

The Journal of chemical physics, 1996-10, Vol.105 (16), p.7064-7078

1996

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Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Paths

The journal of physical chemistry. B, 2005-04, Vol.109 (14), p.6722-6731

2005

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On the Nonpolar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute−Solvent Interaction Energy

Journal of the American Chemical Society, 2003-08, Vol.125 (31), p.9523-9530

2003

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The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators

Journal of computational chemistry, 2002-04, Vol.23 (5), p.517-529

2002

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On the application of numerical analytic continuation methods to the study of quantum mechanical vibrational relaxation processes

The Journal of chemical physics, 1998-11, Vol.109 (18), p.7745-7755

1998

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Free energy surfaces of β-hairpin and α-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

Proteins, structure, function, and bioinformatics, 2004-08, Vol.56 (2), p.310-321

2004

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The simulation of electronic absorption spectrum of a chromophore coupled to a condensed phase environment: Maximum entropy versus singular value decomposition approaches

The Journal of chemical physics, 1997-12, Vol.107 (22), p.9312-9318

1997

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Conformational Equilibria and Free Energy Profiles for the Allosteric Transition of the Ribose-binding Protein

Journal of molecular biology, 2005-10, Vol.353 (1), p.196-210

2005

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In Silico Vaccine Design Based on Molecular Simulations of Rhinovirus Chimeras Presenting HIV-1 gp41 Epitopes

Journal of molecular biology, 2009-01, Vol.385 (2), p.675-691

2009

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Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects

Annual review of physical chemistry, 1998-01, Vol.49 (1), p.531-567

1998

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Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized born solvent model

Proteins, structure, function, and bioinformatics, 2002-08, Vol.48 (2), p.404-422

2002

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A Model for Studying Drying at Hydrophobic Interfaces: Structural and Thermodynamic Properties

The journal of physical chemistry. B, 2001-07, Vol.105 (28), p.6745-6753

2001

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The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute–solvent van der Waals interactions

Biophysical chemistry, 2004-05, Vol.109 (2), p.251-260

2004

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Entropy−Enthalpy Compensation in Solvation and Ligand Binding Revisited

Journal of the American Chemical Society, 1998-05, Vol.120 (18), p.4526-4527

1998

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Thermogravimetric and Spectroscopic Analysis of 8-Hydroxyquinoline 5-Sulphonic Acid-melamine-formaldehyde Polymer Resin-IV

ISRN Thermodynamics, 2012-02, Vol.2012 (2012), p.1-8

2012

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On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models

The Journal of chemical physics, 1998-09, Vol.109 (12), p.4864-4872

1998

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Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation: Application to Amines, Oxides, and Sulfides

The journal of physical chemistry. B, 1997-12, Vol.101 (49), p.10527-10534

1997

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Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications

2006 International Conference on Parallel Processing (ICPP'06), 2006, p.127-134

2006

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Recent Advances in Computational Models for the Study of Protein-Peptide Interactions

Enthalpy−Entropy and Cavity Decomposition of Alkane Hydration Free Energies: Numerical Results and Implications for Theories of Hydrophobic Solvation

Synthesis and biological assessment of 3,7-dihydroxytropolones

AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling

Integrated Modeling Program, Applied Chemical Theory (IMPACT)

The absorption spectrum of the solvated electron in fluid helium by maximum entropy inversion of imaginary time correlation functions from path integral Monte Carlo simulations

On the calculation of dynamical properties of solvated electrons by maximum entropy analytic continuation of path integral Monte Carlo data

Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Paths

On the Nonpolar Hydration Free Energy of Proteins: Surface Area and Continuum Solvent Models for the Solute−Solvent Interaction Energy

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators

On the application of numerical analytic continuation methods to the study of quantum mechanical vibrational relaxation processes

Free energy surfaces of β-hairpin and α-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model

The simulation of electronic absorption spectrum of a chromophore coupled to a condensed phase environment: Maximum entropy versus singular value decomposition approaches

Conformational Equilibria and Free Energy Profiles for the Allosteric Transition of the Ribose-binding Protein

In Silico Vaccine Design Based on Molecular Simulations of Rhinovirus Chimeras Presenting HIV-1 gp41 Epitopes

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects

Synthesis and biological assessment of 3,7-dihydroxytropolonesElectronic supplementary information (ESI) available. See DOI: 10.1039/C7OB02453C

Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized born solvent model

A Model for Studying Drying at Hydrophobic Interfaces: Structural and Thermodynamic Properties

The non-polar solvent potential of mean force for the dimerization of alanine dipeptide: the role of solute–solvent van der Waals interactions

Entropy−Enthalpy Compensation in Solvation and Ligand Binding Revisited

Thermogravimetric and Spectroscopic Analysis of 8-Hydroxyquinoline 5-Sulphonic Acid-melamine-formaldehyde Polymer Resin-IV

On the local and nonlocal components of solvation thermodynamics and their relation to solvation shell models

Thermodynamic Decomposition of Hydration Free Energies by Computer Simulation: Application to Amines, Oxides, and Sulfides

Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications

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