ReviewBiophysical reviews2019
Molecular simulations by generalized-ensemble algorithms in isothermal-isobaric ensemble.
Review in Biophysical reviews, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- RNA G-quadruplex structure recognition by chimeric peptides.Nucleic acids research · 2026Article
- Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency.Journal of computational chemistry · 2023Article
- Structural evolution of Delta lineage of SARS-CoV-2.International journal of biological macromolecules · 2023Article
- Inhibition of amyloid-β(16-22) aggregation by polyphenols using replica permutation with solute tempering molecular dynamics simulation.Biophysics and physicobiology · 2023Article
- Article
- Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation.Molecules (Basel, Switzerland) · 2022Review
- Molecular dynamics simulations of amyloid-β peptides in heterogeneous environments.Biophysics and physicobiology · 2022Article
- All-Atom Molecular Dynamics Simulation Methods for the Aggregation of Protein and Peptides: Replica Exchange/Permutation and Nonequilibrium Simulations.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Promotion and Inhibition of Amyloid-β Peptide Aggregation: Molecular Dynamics Studies.International journal of molecular sciences · 2021Review
- 2019-A year in Biophysical Reviews.Biophysical reviews · 2019Article
- Editorial: Special issue of Biophysical Reviews dedicated to the joint 10th Asian Biophysics Association Symposium and 42nd Australian Society for Biophysics Meeting, Melbourne, Australia, December 2-6, 2018.Biophysical reviews · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Generalized-ensemble algorithms are powerful techniques for investigating biomolecules such as protein, DNA, lipid membrane, and glycan. The generalized-ensemble algorithms were originally developed in the canonical ensemble. On the other hand, not only temperature but also pressure is controlled in experiments. Additionally, pressure is used as perturbation to study relationship between function and structure of biomolecules. For this reason, it is important to perform efficient conformation sampling based on the isothermal-isobaric ensemble. In this article, we review a series of the generalized-ensemble algorithms in the isothermal-isobaric ensemble: multibaric-multithermal, pressure- and temperature-simulated tempering, replica-exchange, and replica-permutation methods. These methods achieve more efficient simulation than the conventional isothermal-isobaric simulation. Furthermore, the isothermal-isobaric generalized-ensemble simulation samples conformations of biomolecules from wider range of temperature and pressure. Thus, we can estimate physical quantities more accurately at any temperature and pressure values. The applications to the biomolecular system are also presented.
Indexed as
Identifiers
What 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.