ArticleJournal of the American Chemical Society2018
Why Does RNA Collapse? The Importance of Water in a Simulation Study of Helix-Junction-Helix Systems.
Article in Journal of the American Chemical Society, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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.
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Who cites it
8 citing papers in PubMed, 23 citations in OpenAlex.
- Exploring Biomolecular Conformational Dynamics with Polarizable Force Field AMOEBA and Enhanced Sampling Method Milestoning.Journal of chemical theory and computation · 2024Article
- Energy landscapes of homopolymeric RNAs revealed by deep unsupervised learning.Biophysical journal · 2024Article
- Perspective: Path Sampling Methods Applied to Enzymatic Catalysis.Journal of chemical theory and computation · 2022Review
- Arrangement of Hydrogen Bonds in Aqueous Solutions of Different Globular Proteins.International journal of molecular sciences · 2022Article
- Refining the RNA Force Field with Small-Angle X-ray Scattering of Helix-Junction-Helix RNA.The journal of physical chemistry letters · 2022Article
- Article
- Machine learning deciphers structural features of RNA duplexes measured with solution X-ray scattering.IUCrJ · 2020Article
- ScMile: A Script to Investigate Kinetics with Short Time Molecular Dynamics Trajectories and the Milestoning Theory.Journal of chemical theory and computation · 2020Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Using computer simulations, we consider the balance of thermodynamic forces that collapse RNA. A model helix-junction-helix (HJH) construct is used to investigate the transition from an extended to a collapsed conformation. Conventional Molecular Dynamics and Milestoning Simulations are used to study the free energy profile of the process for two ion concentrations. We illustrate that HJH folds to a collapsed state with two types of counterions (Mg
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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.