ArticleACS omega2020
Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer.
Article in ACS omega, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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Who cites it
10 citing papers in PubMed.
- The Effect of CuACS chemical neuroscience · 2026Article
- Ensemble molecular dynamics for predicting binding energies of DNA intercalators.RSC advances · 2026Article
- Enhancing aptamer selection in alzheimer's disease: integrating structure prediction and molecular dynamics simulations.Scientific reports · 2025Article
- Impact of Replicas and Simulation Length on In Silico Behaviors of a Protein Domain.Chemphyschem : a European journal of chemical physics and physical chemistry · 2025Article
- Virtual screening: hope, hype, and the fine line in between.Expert opinion on drug discovery · 2025Review
- Article
- Article
- Mechanistic Insights of Polyphenolic Compounds from Rosemary Bound to Their Protein Targets Obtained by Molecular Dynamics Simulations and Free-Energy Calculations.Foods (Basel, Switzerland) · 2023Article
- Exploring Structures and Dynamics of Protamine Molecules through Molecular Dynamics Simulations.ACS omega · 2022Article
- Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety.Sensors (Basel, Switzerland) · 2022Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Using multiple independent simulations instead of one long simulation has been shown to improve the sampling performance attained with the molecular dynamics (MD) simulation method. However, it is generally not known how long each independent simulation should be, how many independent simulations should be used, or to what extent either of these factors affects the overall sampling performance achieved for a given system. The goal of the present study was to assess the sampling performance of multiple independent MD simulations, where each independent simulation begins from a different initial molecular conformation. For this purpose, we used an RNA aptamer that is 25 nucleotides long as a case study. The initial conformations of the aptamer are derived from six
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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.