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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

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. II. Backbone-local potentials of coarse-grained O1→4-bonded polyglucose chains

The Journal of chemical physics, 2017-09, Vol.147 (11), p.115101-115101

2017

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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics

Liwo, Adam

Second edition., 2019

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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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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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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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Ab initio Simulations of Protein-Folding Pathways by Molecular Dynamics with the United-Residue Model of Polypeptide Chains

Proceedings of the National Academy of Sciences - PNAS, 2005-02, Vol.102 (7), p.2362-2367

2005

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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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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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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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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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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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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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Conformational Dynamics of the Trp-Cage Miniprotein at Its Folding Temperature

The journal of physical chemistry. B, 2012-06, Vol.116 (23), p.6898-6907

2012

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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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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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Origin of Correlations between Local Conformational States of Consecutive Amino Acid Residues and Their Role in Shaping Protein Structures and in Allostery

The journal of physical chemistry. B, 2022-11, Vol.126 (46), p.9493-9505

2022

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Correction to “Origin of Correlations between Local Conformational States of Consecutive Amino-Acid Residues and Their Role in Shaping Protein Structures and in Allostery”

The journal of physical chemistry. B, 2023-01, Vol.127 (1), p.425-426

2023

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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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Analysis of Procollagen C-Proteinase Enhancer-1/Glycosaminoglycan Binding Sites and of the Potential Role of Calcium Ions in the Interaction

International journal of molecular sciences, 2019-10, Vol.20 (20), p.5021

2019

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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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Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

The Journal of chemical physics, 2016-05, Vol.144 (18), p.184110-184110

2016

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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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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. II. Backbone-local potentials of coarse-grained O1→4-bonded polyglucose chains

Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics

Protein-folding dynamics: overview of molecular simulation techniques

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

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

Ab initio Simulations of Protein-Folding Pathways by Molecular Dynamics with the United-Residue Model of Polypeptide Chains

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

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

Coarse-grained force field: general folding theory

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

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

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

Conformational Dynamics of the Trp-Cage Miniprotein at Its Folding Temperature

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

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

Origin of Correlations between Local Conformational States of Consecutive Amino Acid Residues and Their Role in Shaping Protein Structures and in Allostery

Correction to “Origin of Correlations between Local Conformational States of Consecutive Amino-Acid Residues and Their Role in Shaping Protein Structures and in Allostery”

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

Analysis of Procollagen C-Proteinase Enhancer-1/Glycosaminoglycan Binding Sites and of the Potential Role of Calcium Ions in the Interaction

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

Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

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

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