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Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins

The Journal of chemical physics, 2020-02, Vol.152 (5), p.054902-054902

2020

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UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics

Nucleic acids research, 2018-07, Vol.46 (W1), p.W304-W309

2018

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A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation

The Journal of chemical physics, 2019-04, Vol.150 (15), p.155104-155104

2019

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Theoretical Investigation of the Coronavirus SARS-CoV-2 (COVID-19) Infection Mechanism and Selectivity

Molecules (Basel, Switzerland), 2022-03, Vol.27 (7), p.2080

2022

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Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer

The journal of physical chemistry. B, 2019-09, Vol.123 (37), p.7829-7839

2019

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Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

Proceedings of the National Academy of Sciences - PNAS, 2013-09, Vol.110 (37), p.14936-14941

2013

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Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

Biomolecules (Basel, Switzerland), 2021-09, Vol.11 (9), p.1347

2021

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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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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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Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach

Biomolecules (Basel, Switzerland), 2023-06, Vol.13 (6), p.941

2023

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Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13

Proteins, structure, function, and bioinformatics, 2019-12, Vol.87 (12), p.1283-1297

2019

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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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Experimental and theoretical studies of the spectroscopic properties of simple symmetrically substituted diphenylacetylene derivatives

RSC advances, 2015-01, Vol.5 (37), p.29294-29303

2015

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Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

Proceedings of the National Academy of Sciences - PNAS, 2014-12, Vol.111 (51), p.18243-18248

2014

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Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis

International journal of molecular sciences, 2019-10, Vol.20 (19), p.4747

2019

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Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions

Frontiers in molecular biosciences, 2022-12, Vol.9, p.1071428-1071428

2022

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Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment

Journal of molecular graphics & modelling, 2019-11, Vol.92 (C), p.154-166

2019

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Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model

Biomolecules (Basel, Switzerland), 2022-08, Vol.12 (8), p.1140

2022

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Recent Developments in Data-Assisted Modeling of Flexible Proteins

Frontiers in molecular biosciences, 2021-12, Vol.8, p.765562-765562

2021

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Impact of selected amino acids of HP0377 (Helicobacter pylori thiol oxidoreductase) on its functioning as a CcmG (cytochrome c maturation) protein and Dsb (disulfide bond) isomerase

PloS one, 2018-04, Vol.13 (4), p.e0195358-e0195358

2018

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Exploring the inhibitory potential of in silico -designed small peptides on Helicobacter pylori Hp0231 (DsbK), a periplasmic oxidoreductase involved in disulfide bond formation

Frontiers in molecular biosciences, 2024-01, Vol.10, p.1335704-1335704

2024

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Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field

The Journal of chemical physics, 2001-08, Vol.115 (5), p.2323-2347

2001

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Potential of Mean Force of Hydrophobic Association: Dependence on Solute Size

The journal of physical chemistry. B, 2007-09, Vol.111 (36), p.10765-10774

2007

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Photophysical properties of 3-[2-(N-phenylcarbazolyl)benzoxazol-5-yl]alanine derivatives—experimental and theoretical studies

Photochemical & photobiological sciences, 2013-02, Vol.12 (2), p.284-297

2013

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A Method for Optimizing Potential-Energy Functions by a Hierarchical Design of the Potential-Energy Landscape: Application to the UNRES Force Field

Proceedings of the National Academy of Sciences - PNAS, 2002-02, Vol.99 (4), p.1937-1942

2002

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Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation

Theoretical Investigation of the Coronavirus SARS-CoV-2 (COVID-19) Infection Mechanism and Selectivity

Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer

Lessons from application of the UNRES force field to predictions of structures of CASP10 targets

Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems

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

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

Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach

Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13

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

Experimental and theoretical studies of the spectroscopic properties of simple symmetrically substituted diphenylacetylene derivatives

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements

Processing and Maturation of Cathepsin C Zymogen: A Biochemical and Molecular Modeling Analysis

Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions

Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment

Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model

Recent Developments in Data-Assisted Modeling of Flexible Proteins

Impact of selected amino acids of HP0377 (Helicobacter pylori thiol oxidoreductase) on its functioning as a CcmG (cytochrome c maturation) protein and Dsb (disulfide bond) isomerase

Exploring the inhibitory potential of in silico -designed small peptides on Helicobacter pylori Hp0231 (DsbK), a periplasmic oxidoreductase involved in disulfide bond formation

Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field

Potential of Mean Force of Hydrophobic Association: Dependence on Solute Size

Photophysical properties of 3-[2-(N-phenylcarbazolyl)benzoxazol-5-yl]alanine derivatives—experimental and theoretical studies

A Method for Optimizing Potential-Energy Functions by a Hierarchical Design of the Potential-Energy Landscape: Application to the UNRES Force Field

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