|
| 37371521 | Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach. | | 2023 |
| 36378078 | Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins. | Journal of Computational Chemistry | 2023 |
| 37587433 | Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin. | | 2023 |
| 37338530 | UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales. | | 2023 |
| 36580595 | Opinion: Protein folds vs. protein folding: Differing questions, different challenges. | Proc Natl Acad Sci U S A | 2023 |
| 36548477 | Correction to "Origin of Correlations between Local Conformational States of Consecutive Amino-Acid Residues and Their Role in Shaping Protein Structures and in Allostery". | | 2023 |
| 36799410 | Long-time scale simulations of virus-like particles from three human-norovirus strains. | | 2023 |
| 35167071 | Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field. | Methods in Molecular Biology | 2022 |
| 36367920 | Origin of Correlations between Local Conformational States of Consecutive Amino Acid Residues and Their Role in Shaping Protein Structures and in Allostery. | Journal of Physical Chemistry B | 2022 |
| 36009034 | Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model. | Biomolecules | 2022 |
| 36134668 | A coarse-grained approach to NMR-data-assisted modeling of protein structures. | Journal of Computational Chemistry | 2022 |
| 35408482 | Theoretical Investigation of the Coronavirus SARS-CoV-2 (COVID-19) Infection Mechanism and Selectivity. | Molecules | 2022 |
| 36589235 | Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions. | | 2022 |
| 35025490 | Influence of Temperature and Salt Concentration on the Hydrophobic Interactions of Adamantane and Hexane. | Journal of Physical Chemistry B | 2022 |
| 34845623 | Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field. | Methods in Molecular Biology | 2022 |
| 34419932 | Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment. | Journal of Molecular Graphics and Modelling | 2021 |
| 34048074 | ESCASA: Analytical estimation of atomic coordinates from coarse-grained geometry for nuclear-magnetic-resonance-assisted protein structure modeling. I. Backbone and H protons. | Journal of Computational Chemistry | 2021 |
| 33079977 | UNRES-Dock-protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations. | | 2021 |
| 34572559 | Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems. | Biomolecules | 2021 |
| 34402552 | Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures. | Journal of Computational Chemistry | 2021 |
| 34505054 | Extended disorder at the cell surface: The conformational landscape of the ectodomains of syndecans. | Matrix Biol Plus | 2021 |
| 35004845 | Recent Developments in Data-Assisted Modeling of Flexible Proteins. | Frontiers in Molecular Biosciences | 2021 |
| 31977133 | Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. | Proteins | 2020 |
| 32145953 | 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 |
| 32064469 | Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models. | Physical Chemistry Chemical Physics | 2020 |
| 31999919 | Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13. | J Chem Inf Model | 2020 |
| 32035448 | 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. | Journal of Chemical Physics | 2020 |
| 31194908 | Introduction of Phosphorylated Residues into the UNRES Coarse-Grained Model: Toward Modeling of Signaling Processes. | Journal of Physical Chemistry B | 2019 |
| 31569265 | Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. | Proteins | 2019 |
| 31612567 | Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment. | Proteins | 2019 |
| 31658765 | Analysis of Procollagen C-Proteinase Enhancer-1/Glycosaminoglycan Binding Sites and of the Potential Role of Calcium Ions in the Interaction. | Int J Mol Sci | 2019 |
| 31037754 | Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints. | Journal of Computational Chemistry | 2019 |
| 31080973 | The molecular mechanism of structural changes in the antimicrobial peptide CM15 upon complex formation with drug molecule suramin: a computational analysis. | Physical Chemistry Chemical Physics | 2019 |
| 30866039 | Local and long range potentials for heparin-protein systems for coarse-grained simulations. | Biopolymers | 2019 |
| 31454484 | Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer. | Journal of Physical Chemistry B | 2019 |
| 31005069 | 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-f | Journal of Chemical Physics | 2019 |
| 31376733 | Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment. | Journal of Molecular Graphics and Modelling | 2019 |
| 30945217 | Formation of Secondary and Supersecondary Structure of Proteins as a Result of Coupling Between Local and Backbone-Electrostatic Interactions: A View Through Cluster-Cumulant Scope. | Methods in Molecular Biology | 2019 |
| 29677198 | 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 |
| 30513992 | Reoptimized UNRES Potential for Protein Model Quality Assessment. | Genes | 2018 |
| 30306573 | A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields. | Journal of Computational Chemistry | 2018 |
| 30014063 | Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing. | Physical Chemistry Chemical Physics | 2018 |
| 29967418 | An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. | Sci Rep | 2018 |
| 30049211 | Protein-Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges For Flexible Systems. | Journal of Physical Chemistry B | 2018 |
| 29860162 | Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets. | J Mol Graph Model | 2018 |
| 30082873 | Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners. | Sci Rep | 2018 |
| 29718313 | UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics. | Nucleic Acids Research | 2018 |
| 29134679 | 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 |
| 29283263 | Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. | Journal of Chemical Information and Modeling | 2018 |
| 28093787 | In situ data analytics and indexing of protein trajectories. | Journal of Computational Chemistry | 2017 |