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Protein-folding dynamics: overview of molecular simulation techniques

Annual review of physical chemistry, 2007-01, Vol.58 (1), p.57-83

2007

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Curvature and Torsion of Protein Main Chain as Local Order Parameters of Protein Unfolding

The journal of physical chemistry. B, 2020-06, Vol.124 (22), p.4391-4398

2020

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Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics

Journal of chemical information and modeling, 2017-09, Vol.57 (9), p.2364-2377

2017

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Relation between Free Energy Landscapes of Proteins and Dynamics

Journal of chemical theory and computation, 2010-02, Vol.6 (2), p.583-595

2010

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Dependence of the Formation of Tau and Aβ Peptide Mixed Aggregates on the Secondary Structure of the N‑Terminal Region of Aβ

The journal of physical chemistry. B, 2018-07, Vol.122 (28), p.7049-7056

2018

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Coarse-grained force field: general folding theory

Physical chemistry chemical physics : PCCP, 2011-01, Vol.13 (38), p.16890-16901

2011

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Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged–Hydrophobic/Polar and Polar–Hydrophobic/Polar Side Chains

The journal of physical chemistry. B, 2017-01, Vol.121 (2), p.379-390

2017

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Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach

The Journal of chemical physics, 2015-12, Vol.143 (24), p.243111-243111

2015

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DNA Duplex Formation with a Coarse-Grained Model

Journal of chemical theory and computation, 2014-11, Vol.10 (11), p.5020-5035

2014

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My 65 years in protein chemistry

Quarterly reviews of biophysics, 2015-05, Vol.48 (2), p.117-177

Scheraga, Harold A.

2015

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Assessing the One-Bond Cα–H Spin–Spin Coupling Constants in Proteins: Pros and Cons of Different Approaches

The journal of physical chemistry. B, 2020-02, Vol.124 (5), p.735-741

2020

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Potential of Mean Force of Association of Large Hydrophobic Particles: Toward the Nanoscale Limit

The journal of physical chemistry. B, 2010-01, Vol.114 (2), p.993-1003

2010

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Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations

Journal of chemical theory and computation, 2015-02, Vol.11 (2), p.817-831

2015

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Global Optimization of Clusters, Crystals, and Biomolecules

Science (American Association for the Advancement of Science), 1999-08, Vol.285 (5432), p.1368-1372

1999

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A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions

Journal of molecular modeling, 2014-08, Vol.20 (8), p.2306-2306, Article 2306

2014

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A new protein nucleic‐acid coarse‐grained force field based on the UNRES and NARES‐2P force fields

Journal of computational chemistry, 2018-10, Vol.39 (28), p.2360-2370

2018

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Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics

Journal of chemical theory and computation, 2021-05, Vol.17 (5), p.3203-3220

2021

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Insufficiently Dehydrated Hydrogen Bonds as Determinants of Protein Interactions

Proceedings of the National Academy of Sciences - PNAS, 2003-01, Vol.100 (1), p.113-118

2003

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A Study of the α-Helical Intermediate Preceding the Aggregation of the Amino-Terminal Fragment of the β Amyloid Peptide (Aβ1–28)

The journal of physical chemistry. B, 2011-11, Vol.115 (44), p.12978-12983

2011

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Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2010-04, Vol.114 (13), p.4471-4485

2010

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Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics

Journal of chemical theory and computation, 2012-05, Vol.8 (5), p.1750-1764

2012

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Statistical Model To Decipher Protein Folding/Unfolding at a Local Scale

The journal of physical chemistry. B, 2018-04, Vol.122 (13), p.3540-3549

2018

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Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH

Journal of molecular structure, 2017-04, Vol.1134, p.576-581

2017

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Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field

Journal of computational chemistry, 2009-10, Vol.30 (13), p.2127-2135

2009

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New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain

The journal of physical chemistry. B, 2020-05, Vol.124 (19), p.3855-3872

2020

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Protein-folding dynamics: overview of molecular simulation techniques

Curvature and Torsion of Protein Main Chain as Local Order Parameters of Protein Unfolding

Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics

Relation between Free Energy Landscapes of Proteins and Dynamics

Dependence of the Formation of Tau and Aβ Peptide Mixed Aggregates on the Secondary Structure of the N‑Terminal Region of Aβ

Coarse-grained force field: general folding theory

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged–Hydrophobic/Polar and Polar–Hydrophobic/Polar Side Chains

Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach

DNA Duplex Formation with a Coarse-Grained Model

My 65 years in protein chemistry

Assessing the One-Bond Cα–H Spin–Spin Coupling Constants in Proteins: Pros and Cons of Different Approaches

Potential of Mean Force of Association of Large Hydrophobic Particles: Toward the Nanoscale Limit

Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations

Global Optimization of Clusters, Crystals, and Biomolecules

A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions

A new protein nucleic‐acid coarse‐grained force field based on the UNRES and NARES‐2P force fields

Investigation of Phosphorylation-Induced Folding of an Intrinsically Disordered Protein by Coarse-Grained Molecular Dynamics

Insufficiently Dehydrated Hydrogen Bonds as Determinants of Protein Interactions

A Study of the α-Helical Intermediate Preceding the Aggregation of the Amino-Terminal Fragment of the β Amyloid Peptide (Aβ1–28)

Investigation of Protein Folding by Coarse-Grained Molecular Dynamics with the UNRES Force Field

Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics

Statistical Model To Decipher Protein Folding/Unfolding at a Local Scale

Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH

Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field

New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain

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