ReviewBioMed research international2015
Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review.
Review in BioMed research international, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 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
48 citing papers in PubMed.
- Urolithin A alleviates vascular remodeling through mitochondrial SIRT3-mediated SOD2 deacetylation and antioxidation in hypertensive rats.Redox report : communications in free radical research · 2026Article
- DFT, MC, and MD investigation of H₂MoO₄ adsorption on model AISI 304 stainless steel surfaces: effects of inhibitor loading, temperature, and confined shear.Journal of molecular modeling · 2026Article
- Mesoporous Silica with Different Channel Widths for CsMaterials (Basel, Switzerland) · 2026Article
- Determinants of centromeric nucleosome conformation.bioRxiv : the preprint server for biology · 2026Article
- Article
- The contribution of phenolic endocrine-disrupting chemicals to breast cancer risk: A comprehensive bioinformatics analysis.Scientific reports · 2026Article
- Molecular Mechanisms of Gain-of-Function Mutations in λ Cro Revealed by Molecular Dynamics Simulations.ACS physical chemistry Au · 2025Article
- Multiscale molecular dynamics investigation of high-efficiency hydrogen storage in titanium-doped carbon nanotubes.Scientific reports · 2025Article
- Deciphering the molecular mechanisms of BPTF interactions with nucleosomes via molecular simulations.Biophysical journal · 2025Article
- Molecular Simulation of the Isotropic-to-Nematic Transition of Rod-like Polymers in Bulk and Under Confinement.Polymers · 2025Article
- Deciphering the Molecular Mechanisms of BPTF Interactions with Nucleosomes via Molecular Simulations.bioRxiv : the preprint server for biology · 2025Article
- Computational studies on the functional and structural impact of pathogenic mutations in enzymes.Protein science : a publication of the Protein Society · 2025Review
- Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning.Journal of chemical information and modeling · 2025Article
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- Modeling magnetic properties of cobalt nanofilms used as a component of spin hybrid superconductor-ferromagnetic structures.Beilstein journal of nanotechnology · 2025Article
- Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells.Journal of chemical information and modeling · 2024Review
- Identification of metabolites from the gut microbiota in hypertension via network pharmacology and molecular docking.Bioresources and bioprocessing · 2024Article
- Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning.Research square · 2024Article
- Article
- Special Issue "Third Edition: Advances in Molecular Simulation".International journal of molecular sciences · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods.
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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.