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Principal Component Analysis for Protein Folding Dynamics

Journal of molecular biology, 2009-01, Vol.385 (1), p.312-329

2009

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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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Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix

Physical review letters, 2013-02, Vol.110 (9), p.098101-098101, Article 098101

2013

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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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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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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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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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Computational techniques for efficient conformational sampling of proteins

Current opinion in structural biology, 2008-04, Vol.18 (2), p.134-139

2008

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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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Mechanism of Fiber Assembly: Treatment of Aβ Peptide Aggregation with a Coarse-Grained United-Residue Force Field

Journal of molecular biology, 2010-12, Vol.404 (3), p.537-552

2010

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Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2340, p.79

2022

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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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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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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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Proline Cis−Trans Isomerization and Protein Folding

Biochemistry (Easton), 2002-12, Vol.41 (50), p.14637-14644

2002

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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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Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches

Proteins, structure, function, and bioinformatics, 2015-08, Vol.83 (8), p.1414-1426

2015

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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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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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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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Principal Component Analysis for Protein Folding Dynamics

Protein-folding dynamics: overview of molecular simulation techniques

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

Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix

Relation between Free Energy Landscapes of Proteins and Dynamics

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

DNA Duplex Formation with a Coarse-Grained Model

Computational techniques for efficient conformational sampling of proteins

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

Mechanism of Fiber Assembly: Treatment of Aβ Peptide Aggregation with a Coarse-Grained United-Residue Force Field

Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field

My 65 years in protein chemistry

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

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

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

Proline Cis−Trans Isomerization and Protein Folding

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

Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches

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

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

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

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