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The structure of protein dynamic space

Proceedings of the National Academy of Sciences - PNAS, 2020-08, Vol.117 (33), p.19938-19942

2020

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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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George Hess: A scientific appreciation

Proceedings of the National Academy of Sciences - PNAS, 2016-02, Vol.113 (6), p.1466-1467

Scheraga, Harold A.

2016

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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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Global informatics and physical property selection in protein sequences

Proceedings of the National Academy of Sciences - PNAS, 2016-02, Vol.113 (7), p.1808-1810

2016

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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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Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences

Proceedings of the National Academy of Sciences - PNAS, 2014-04, Vol.111 (14), p.5225-5229

2014

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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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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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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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Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH

Proceedings of the National Academy of Sciences - PNAS, 2011-04, Vol.108 (14), p.5602-5607

2011

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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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Lysosomal enzyme tripeptidyl peptidase 1 destabilizes fibrillar Aβ by multiple endoproteolytic cleavages within the β-sheet domain

Proceedings of the National Academy of Sciences - PNAS, 2018-02, Vol.115 (7), p.1493-1498

2018

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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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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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Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state

Proceedings of the National Academy of Sciences - PNAS, 2012-06, Vol.109 (26), p.10346-10351

2012

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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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The structure of protein dynamic space

Protein-folding dynamics: overview of molecular simulation techniques

George Hess: A scientific appreciation

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

Global informatics and physical property selection in protein sequences

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

Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences

DNA Duplex Formation with a Coarse-Grained Model

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

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

Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH

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

Lysosomal enzyme tripeptidyl peptidase 1 destabilizes fibrillar Aβ by multiple endoproteolytic cleavages within the β-sheet domain

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

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)

Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state

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

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