ArticleNucleic acids research2013
NAFlex: a web server for the study of nucleic acid flexibility.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation.Nature communications · 2026Article
- MDNA : a software module for DNA structure generation and analysis.Nucleic acids research · 2026Article
- Linker histone H1 functions as a liquid-like glue to organize chromatin in living human cells.Science advances · 2026Article
- H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations.Molecular cell · 2026Article
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- Nucleosome spacing can fine-tune higher-order chromatin assembly.Nature communications · 2025Article
- Cold-induced nucleosome dynamics linked to silencing of Arabidopsis FLC.Nature communications · 2025Article
- Systematic study of hybrid triplex topology and stability suggests a general triplex-mediated regulatory mechanism.Nucleic acids research · 2025Article
- Relative genotoxicity of polycyclic aromatic hydrocarbons inferred from free energy perturbation approaches.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage φ29.Nucleic acids research · 2024Article
- Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides.Nucleic acids research · 2023Article
- Effect of cetrimonium carrier micelles on bacterial membranes and extracellular DNA, an in silico study.Scientific reports · 2023Article
- Correlated motions in DNA: beyond base-pair step models of DNA flexibility.Nucleic acids research · 2023Article
- How acidic amino acid residues facilitate DNA target site selection.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.Wiley interdisciplinary reviews. Computational molecular science · 2022Article
- DNA-MBF1 study using molecular dynamics simulations : On the road to understanding the heat stress response in DNA-protein interactions in plants.European biophysics journal : EBJ · 2021Article
- Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions.Nature communications · 2021Article
- DNA binds to a specific site of the adhesive blood-protein von Willebrand factor guided by electrostatic interactions.Nucleic acids research · 2020Article
- A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level.Nucleic acids research · 2020Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present NAFlex, a new web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server allows the user to incorporate structures from protein data banks, completing gaps and removing structural inconsistencies. It is also possible to define canonical (average or sequence-adapted) nucleic acid structures using a variety of predefined internal libraries, as well to create specific nucleic acid conformations from the sequence. The server offers a variety of methods to explore nucleic acid flexibility, such as a colorless wormlike-chain model, a base-pair resolution mesoscopic model and atomistic molecular dynamics simulations with a wide variety of protocols and force fields. The trajectories obtained by simulations, or imported externally, can be visualized and analyzed using a large number of tools, including standard Cartesian analysis, essential dynamics, helical analysis, local and global stiffness, energy decomposition, principal components and in silico NMR spectra. The server is accessible free of charge from the mmb.irbbarcelona.org/NAFlex webpage.
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