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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations

Bioinformatics (Oxford, England), 2021-07, Vol.37 (11), p.1613-1615

2021

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Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose

Nanoscale, 2017-01, Vol.9 (29), p.10263-10276

2017

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Prediction of protein structure with the coarse‐grained UNRES force field assisted by small X‐ray scattering data and knowledge‐based information

Proteins, structure, function, and bioinformatics, 2018-03, Vol.86 (S1), p.228-239

2018

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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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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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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2376, p.399

2022

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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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Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A

Journal of chemical theory and computation, 2017-11, Vol.13 (11), p.5721-5730

2017

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Performance of protein-structure predictions with the physics-based UNRES force field in CASP11

Bioinformatics (Oxford, England), 2016-11, Vol.32 (21), p.3270-3278

2016

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Reoptimized UNRES Potential for Protein Model Quality Assessment

Genes, 2018-12, Vol.9 (12), p.601

2018

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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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Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13

Journal of chemical information and modeling, 2020-03, Vol.60 (3), p.1844-1864

2020

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Extension of coarse-grained UNRES force field to treat carbon nanotubes

Journal of molecular modeling, 2018-05, Vol.24 (5), p.121-12, Article 121

2018

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Preventing fibril formation of a protein by selective mutation

Proceedings of the National Academy of Sciences - PNAS, 2015-11, Vol.112 (44), p.13549-13554

2015

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Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field

Journal of chemical information and modeling, 2016-11, Vol.56 (11), p.2263-2279

2016

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Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field

Journal of chemical information and modeling, 2015-06, Vol.55 (6), p.1271-1281

2015

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Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival

Scientific reports, 2018-03, Vol.8 (1), p.4390-12, Article 4390

2018

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Ergodicity and model quality in template‐restrained canonical and temperature/Hamiltonian replica exchange coarse‐grained molecular dynamics simulations of proteins

Journal of computational chemistry, 2017-12, Vol.38 (31), p.2730-2746

2017

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Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets

Journal of molecular graphics & modelling, 2018-08, Vol.83, p.92-99

2018

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WeFold: A coopetition for protein structure prediction

Proteins, structure, function, and bioinformatics, 2014-09, Vol.82 (9), p.1850-1868

2014

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Role of the sulfur to α-carbon thioether bridges in thurincin H

Journal of biomolecular structure & dynamics, 2017-10, Vol.35 (13), p.2868-2879

2017

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Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers

Progress in molecular biology and translational science, 2020, Vol.170, p.73-122

2020

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Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field

Journal of molecular modeling, 2015-03, Vol.21 (3), p.64-64, Article 64

2015

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Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from S accharomyces cerevisiae by all-atom and coarse-grained approaches: Modeling of Isu1 to Jac1 Binding

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

2015

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Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purposeElectronic supplementary information (ESI) available. See DOI: 10.1039/c7nr00770a

2017-07

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UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations

Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose

Prediction of protein structure with the coarse‐grained UNRES force field assisted by small X‐ray scattering data and knowledge‐based information

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

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

Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field

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

Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11

Reoptimized UNRES Potential for Protein Model Quality Assessment

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

Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13

Extension of coarse-grained UNRES force field to treat carbon nanotubes

Preventing fibril formation of a protein by selective mutation

Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field

Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival

Ergodicity and model quality in template‐restrained canonical and temperature/Hamiltonian replica exchange coarse‐grained molecular dynamics simulations of proteins

Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets

WeFold: A coopetition for protein structure prediction

Role of the sulfur to α-carbon thioether bridges in thurincin H

Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers

Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field

Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from S accharomyces cerevisiae by all-atom and coarse-grained approaches: Modeling of Isu1 to Jac1 Binding

Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purposeElectronic supplementary information (ESI) available. See DOI: 10.1039/c7nr00770a

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