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Introducing Titratable Water to All-Atom Molecular Dynamics at Constant pH

Biophysical journal, 2013-08, Vol.105 (4), p.L15-L17

2013

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Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

The Journal of chemical physics, 2012-11, Vol.137 (18), p.184105-184105

2012

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Thermodynamic Coupling of Protonation and Conformational Equilibria in Proteins: Theory and Simulation

Biophysical journal, 2012-04, Vol.102 (7), p.1590-1597

2012

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Uncovering Specific Electrostatic Interactions in the Denatured States of Proteins

Biophysical journal, 2010-08, Vol.99 (3), p.924-932

Shen, Jana K.

2010

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Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics

Journal of computational chemistry, 2014-10, Vol.35 (27), p.1986-1996

2014

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Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids

The Journal of chemical physics, 2012-11, Vol.137 (19), p.194902-194902

2012

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Mechanism of the pH-Controlled Self-Assembly of Nanofibers from Peptide Amphiphiles

Journal of physical chemistry. C, 2014-07, Vol.118 (29), p.16272-16278

2014

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Unraveling a Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins

The journal of physical chemistry letters, 2012-03, Vol.3 (5), p.658-662

2012

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Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

Journal of chemical theory and computation, 2011-08, Vol.7 (8), p.2617-2629

2011

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Diarylcyclopentendione Metabolite Obtained from a Preussia typharum Isolate Procured Using an Unconventional Cultivation Approach

Journal of natural products (Washington, D.C.), 2012-10, Vol.75 (10), p.1819-1823

2012

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Recent development and application of constant pH molecular dynamics

Molecular simulation, 2014-01, Vol.40 (10-11), p.830-838

2014

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Nitric oxide coupling mediated by iron porphyrins: the N-N bond formation step is facilitated by electrons and a proton

Chemical communications (Cambridge, England), 2012-01, Vol.48 (72), p.9041-9043

2012

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Self-Assembly and Bilayer–Micelle Transition of Fatty Acids Studied by Replica-Exchange Constant pH Molecular Dynamics

Langmuir, 2013-12, Vol.29 (48), p.14823-14830

2013

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A Method To Determine Residue-Specific Unfolded-State pK a Values from Analysis of Stability Changes in Single Mutant Cycles

Journal of the American Chemical Society, 2010-06, Vol.132 (21), p.7258-7259

Shen, Jana K

2010

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Probing the Strand Orientation and Registry Alignment in the Propagation of Amyloid Fibrils

Biochemistry (Easton), 2010-06, Vol.49 (25), p.5290-5298

2010

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Simulating pH Titration of a Single Surfactant in Ionic and Nonionic Surfactant Micelles

The journal of physical chemistry. B, 2011-12, Vol.115 (50), p.14980-14990

2011

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Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized born implicit-solvent model

Journal of computational chemistry, 2011-08, Vol.32 (11), p.2348-2358

2011

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Predicting proton titration in cationic micelle and bilayer environments

The Journal of chemical physics, 2014-08, Vol.141 (8), p.084714-084714

2014

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Nucleotide Dynamics at the A-Site Cleft in the Peptidyltransferase Center of H. marismortui 50S Ribosomal Subunits

The journal of physical chemistry letters, 2012-04, Vol.3 (8), p.1007-1010

2012

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Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy

Proteins, structure, function, and bioinformatics, 2011-12, Vol.79 (12), p.3364-3373

2011

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Progress in the prediction of pKa values in proteins

Proteins, structure, function, and bioinformatics, 2011-12, Vol.79 (12), p.3260-3275

2011

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Predicting pKa Values with Continuous Constant pH Molecular Dynamics

Biothermodynamics, Part B, 2009, Vol.466, p.455-475

2009

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Mechanism of Proton Transport of the M2 Proton Channel Studied by Constant pH Molecular Dynamics

Biophysical journal, 2015-01, Vol.108 (2), p.439a-439a

2015

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A Method To Determine Residue-Specific Unfolded-State p K a Values from Analysis of Stability Changes in Single Mutant Cycles

Journal of the American Chemical Society, 2010-06, Vol.132 (21), p.7258-7259

Shen, Jana K.

2010

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Titration Properties and pH-Dependent Aggregation of Chitosan

Biophysical journal, 2015-01, Vol.108 (2), p.488a-488a

2015

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Introducing Titratable Water to All-Atom Molecular Dynamics at Constant pH

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

Thermodynamic Coupling of Protonation and Conformational Equilibria in Proteins: Theory and Simulation

Uncovering Specific Electrostatic Interactions in the Denatured States of Proteins

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics

Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids

Mechanism of the pH-Controlled Self-Assembly of Nanofibers from Peptide Amphiphiles

Unraveling a Trap-and-Trigger Mechanism in the pH-Sensitive Self-Assembly of Spider Silk Proteins

Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

Diarylcyclopentendione Metabolite Obtained from a Preussia typharum Isolate Procured Using an Unconventional Cultivation Approach

Recent development and application of constant pH molecular dynamics

Nitric oxide coupling mediated by iron porphyrins: the N-N bond formation step is facilitated by electrons and a proton

Self-Assembly and Bilayer–Micelle Transition of Fatty Acids Studied by Replica-Exchange Constant pH Molecular Dynamics

A Method To Determine Residue-Specific Unfolded-State pK a Values from Analysis of Stability Changes in Single Mutant Cycles

Probing the Strand Orientation and Registry Alignment in the Propagation of Amyloid Fibrils

Simulating pH Titration of a Single Surfactant in Ionic and Nonionic Surfactant Micelles

Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized born implicit-solvent model

Predicting proton titration in cationic micelle and bilayer environments

Nucleotide Dynamics at the A-Site Cleft in the Peptidyltransferase Center of H. marismortui 50S Ribosomal Subunits

Toward accurate prediction of pKa values for internal protein residues: The importance of conformational relaxation and desolvation energy

Progress in the prediction of pKa values in proteins

Predicting pKa Values with Continuous Constant pH Molecular Dynamics

Mechanism of Proton Transport of the M2 Proton Channel Studied by Constant pH Molecular Dynamics

A Method To Determine Residue-Specific Unfolded-State p K a Values from Analysis of Stability Changes in Single Mutant Cycles

Titration Properties and pH-Dependent Aggregation of Chitosan

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