ArticleMethods in molecular biology (Clifton, N.J.)2022
Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.
Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- Advances and opportunities for computational interrogation of plant proteins.The Plant journal : for cell and molecular biology · 2026Review
- Implementation of Replica-Averaged Restraints from Nuclear Magnetic Resonance Measurement with UNRES Coarse Grained Model of Polypeptide Chains.Molecules (Basel, Switzerland) · 2025Article
- Hydrophobic and Electrostatic Sequence Patterning Directs Hierarchical Assembly of Phenylalanine-Rich Oligopeptides.The journal of physical chemistry letters · 2025Article
- Recapturing Cooperativity of α-Helix Formation and Packing in Coarse-Grained Protein Structure Modeling with Multitorsional Potentials.The journal of physical chemistry. B · 2025Article
- Two Methods for Superposing the Structures of Like-Molecule Assemblies: Application to Peptide and Protein Oligomers and Aggregates.Molecules (Basel, Switzerland) · 2025Article
- Implementation of Time-Averaged Restraints with UNRES Coarse-Grained Model of Polypeptide Chains.Journal of chemical theory and computation · 2025Article
- Design and Characterization of Antibacterial Peptide Nanofibrils as Components of Composites for Biomaterial Applications.Current protein & peptide science · 2025Article
- Coarse-Grained Simulation Study of the Association of Selected Dipeptides.The journal of physical chemistry. B · 2024Article
- A coarse-grained model for disordered and multi-domain proteins.Protein science : a publication of the Protein Society · 2024Article
- Integrating Explicit and Implicit Fullerene Models into UNRES Force Field for Protein Interaction Studies.Molecules (Basel, Switzerland) · 2024Article
- Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures.Journal of chemical information and modeling · 2024Article
- Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches.The journal of physical chemistry letters · 2023Review
- Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach.Biomolecules · 2023Article
- Application of molecular dynamics simulation in self-assembled cancer nanomedicine.Biomaterials research · 2023Review
- A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution.Frontiers in bioinformatics · 2023Article
- 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 · 2022Article
- Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model.Biomolecules · 2022Article
- Automated Protein Secondary Structure Assignment from CBiomolecules · 2022Article
- Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions.Frontiers in molecular biosciences · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics and its replica-exchange extensions, UNRES has found a variety of applications, including ab initio and database-assisted protein-structure prediction, simulating protein-folding pathways, exploring protein free-energy landscapes, and solving biological problems. This chapter provides a summary of UNRES and a guide for potential users regarding the application of the UNRES package in a variety of research tasks.
Indexed as
Identifiers
34845623What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.