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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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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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Molecular dynamics study of the internal water molecules in vasopressin and oxytocin receptors

Protein and peptide letters, 2009-04, Vol.16 (4), p.342

2009

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Multi-GPU-powered UNRES package for physics-based coarse-grained simulations of structure, dynamics, and thermodynamics of protein systems at biological size- and timescales

Biophysical journal, 2024-02, Vol.123 (3), p.422a-422a

2024

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Interactions of vasopressin and oxytocin receptors with vasopressin analogues substituted in position 2 with 3,3′-diphenylalanine - a molecular docking study

Journal of peptide science, 2013-02, Vol.19 (2), p.118-126

2013

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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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Molecular modeling of the neurohypophyseal receptor/atosiban complexes

Protein and peptide letters, 2003-06, Vol.10 (3), p.295

2003

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Molecular Docking-Based Study of Vasopressin Analogues Modified at Positions 2 and 3 with N-Methylphenylalanine: Influence on Receptor-Bound Conformations and Interactions with Vasopressin and Oxytocin Receptors

Journal of medicinal chemistry, 2006-04, Vol.49 (8), p.2463-2469

2006

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Influence of bulky 3,3′-diphenylalanine enantiomers replacing position 2 of AVP analogues on their conformations: NMR and molecular modeling studies

European journal of medicinal chemistry, 2010-09, Vol.45 (9), p.4065-4073

2010

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Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems

Biophysical journal, 2021-02, Vol.120 (3), p.83a-84a

2021

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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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Conformational stability of the full-atom hexameric model of the ClpB chaperone from Escherichia coli

Biopolymers, 2010-01, Vol.93 (1), p.47-60

2010

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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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NMR and MD Analysis of the Bonding Interaction of Vancomycin with Muramyl Pentapeptide

International journal of molecular sciences, 2022-01, Vol.23 (3), p.1146

2022

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Efficient synthesis and antifungal investigation of nucleosides’ quaternaryammonium salt derivatives

Turkish journal of chemistry, 2019-02, Vol.43 (1), p.157-171

2019

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The Quaternization Reaction of 5- O -Sulfonates of Methyl 2,3- o -Isopropylidene- β -D-Ribofuranoside With Selected Heterocyclic and Aliphatic Amines

Molecules (Basel, Switzerland), 2020-05, Vol.25 (9), p.2161

2020

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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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Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment

Journal of molecular graphics & modelling, 2021-11, Vol.108, p.108008-108008, Article 108008

2021

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Molecular modeling of Gram-positive bacteria peptidoglycan layer, selected glycopeptide antibiotics and vancomycin derivatives modified with sugar moieties

Carbohydrate research, 2014-05, Vol.389, p.154-164

2014

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Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin-modeling of an activated state

Journal of peptide science, 2006-03, Vol.12 (3), p.171-179

2006

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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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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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Interaction of class A G protein-coupled receptors with G proteins

Acta biochimica Polonica, 2004-01, Vol.51 (1), p.129-136

2004

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Investigation of cis/trans ratios of peptide bonds in AVP analogues containing N-methylphenylalanine enantiomers

Journal of peptide science, 2006-01, Vol.12 (1), p.13-24

2006

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A hypothesis for GPCR activation

Journal of molecular modeling, 2005-09, Vol.11 (4-5), p.407-415

2005

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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

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

Molecular dynamics study of the internal water molecules in vasopressin and oxytocin receptors

Multi-GPU-powered UNRES package for physics-based coarse-grained simulations of structure, dynamics, and thermodynamics of protein systems at biological size- and timescales

Interactions of vasopressin and oxytocin receptors with vasopressin analogues substituted in position 2 with 3,3′-diphenylalanine - a molecular docking study

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

Molecular modeling of the neurohypophyseal receptor/atosiban complexes

Molecular Docking-Based Study of Vasopressin Analogues Modified at Positions 2 and 3 with N-Methylphenylalanine: Influence on Receptor-Bound Conformations and Interactions with Vasopressin and Oxytocin Receptors

Influence of bulky 3,3′-diphenylalanine enantiomers replacing position 2 of AVP analogues on their conformations: NMR and molecular modeling studies

Extension of the Unres Package for Physics-Based Coarse-Grained Simulations of Proteins and Protein Complexes to Very Large Systems

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

Conformational stability of the full-atom hexameric model of the ClpB chaperone from Escherichia coli

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

NMR and MD Analysis of the Bonding Interaction of Vancomycin with Muramyl Pentapeptide

Efficient synthesis and antifungal investigation of nucleosides’ quaternaryammonium salt derivatives

The Quaternization Reaction of 5- O -Sulfonates of Methyl 2,3- o -Isopropylidene- β -D-Ribofuranoside With Selected Heterocyclic and Aliphatic Amines

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

Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment

Molecular modeling of Gram-positive bacteria peptidoglycan layer, selected glycopeptide antibiotics and vancomycin derivatives modified with sugar moieties

Molecular dynamics simulation of human neurohypophyseal hormone receptors complexed with oxytocin-modeling of an activated state

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

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

Interaction of class A G protein-coupled receptors with G proteins

Investigation of cis/trans ratios of peptide bonds in AVP analogues containing N-methylphenylalanine enantiomers

A hypothesis for GPCR activation

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