ArticleJournal of chemical theory and computation2015
Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and Their Complexes with Proteins.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 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
50 citing papers in PubMed.
- Integrative Network Pharmacology and Molecular Docking Analysis Reveals the Multitarget Mechanisms of Pterostilbene in Neurodegenerative Diseases.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Determinants of centromeric nucleosome conformation.bioRxiv : the preprint server for biology · 2026Article
- Rectifying AI-generated protein structure ensembles for equilibrium using physics-based computations.bioRxiv : the preprint server for biology · 2026Article
- Characterisation of an unusual nicotinic acetylcholine receptor subtype preferentially sensitive to biogenic amines.Communications biology · 2025Article
- Molecular Mechanisms of Gain-of-Function Mutations in λ Cro Revealed by Molecular Dynamics Simulations.ACS physical chemistry Au · 2025Article
- Molecular Dynamics Simulations of RNA Stem-Loop Folding Using an Atomistic Force Field and a Generalized Born Implicit Solvent.ACS omega · 2025Article
- Deciphering the molecular mechanisms of BPTF interactions with nucleosomes via molecular simulations.Biophysical journal · 2025Article
- Pathway regulation mechanism by cotranslational protein folding.Communications chemistry · 2025Article
- Hierarchical Extended Linkage Method (HELM)'s Deep Dive into Hybrid Clustering Strategies.Journal of chemical information and modeling · 2025Article
- Increased functional unit flexibility and solvent accessibility favours oxygen capture in molluscan hemocyanin.RSC advances · 2025Article
- Deciphering the Molecular Mechanisms of BPTF Interactions with Nucleosomes via Molecular Simulations.bioRxiv : the preprint server for biology · 2025Article
- Article
- MELD in Action: Harnessing Data to Accelerate Molecular Dynamics.Journal of chemical information and modeling · 2025Review
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Dimerization of the deaminase domain and locking interactions with Cas9 boost base editing efficiency in ABE8e.Nucleic acids research · 2024Article
- Force Field Limitations of All-Atom Continuous Constant pH Molecular Dynamics.The journal of physical chemistry. B · 2024Article
- Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.Journal of chemical information and modeling · 2024Article
- Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs.Journal of chemical theory and computation · 2024Article
- Assessing RNA atomistic force fields via energy landscape explorations in implicit solvent.Biophysical reviews · 2024Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
The Generalized Born (GB) implicit solvent model has undergone significant improvements in accuracy for modeling of proteins and small molecules. However, GB still remains a less widely explored option for nucleic acid simulations, in part because fast GB models are often unable to maintain stable nucleic acid structures or they introduce structural bias in proteins, leading to difficulty in application of GB models in simulations of protein-nucleic acid complexes. Recently, GB-neck2 was developed to improve the behavior of protein simulations. In an effort to create a more accurate model for nucleic acids, a similar procedure to the development of GB-neck2 is described here for nucleic acids. The resulting parameter set significantly reduces absolute and relative energy error relative to Poisson-Boltzmann for both nucleic acids and nucleic acid-protein complexes, when compared to its predecessor GB-neck model. This improvement in solvation energy calculation translates to increased structural stability for simulations of DNA and RNA duplexes, quadruplexes, and protein-nucleic acid complexes. The GB-neck2 model also enables successful folding of small DNA and RNA hairpins to near native structures as determined from comparison with experiment. The functional form and all required parameters are provided here and also implemented in the AMBER software.
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.