ArticleNucleic acids research2020
DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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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
40 citing papers in PubMed, 52 citations in OpenAlex.
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- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
- CoBRA: compound binding site prediction using RNA language model.Briefings in bioinformatics · 2026Article
- Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.Computational and structural biotechnology journal · 2026Article
- Quadrupia provides a comprehensive catalog of G-quadruplexes across genomes from the tree of life.Genome research · 2025Article
- PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures.PLoS computational biology · 2025Article
- Single-cell stemness analysis highlights Midkine-LRP1 pathway and identifies new bladder cancer subtypes.Cancer cell international · 2025Article
- Berbamine Targets TNFAIP3: A Bioactive Compound Alleviates Oxidative Stress and Inflammation in the Comorbidity of Insomnia and Chronic Obstructive Pulmonary Disease Through Multi-Omics Integration.International journal of molecular sciences · 2025Article
- G4STAB: a multi-input deep learning model to predict G-quadruplex thermodynamic stability based on sequence and salt concentration.Bioinformatics (Oxford, England) · 2025Article
- RNA language model and graph attention network for RNA and small molecule binding sites prediction.Bioinformatics (Oxford, England) · 2025Article
- rsRNASP1: A distance- and dihedral-dependent statistical potential for RNA 3D structure evaluation.Biophysical journal · 2025Article
- ARTEM: a method for RNA and DNA tertiary motif identification with backbone permutations.Genome biology · 2025Article
- Elucidating the solution structure of the monomolecularChemical science · 2025Article
- GINClus: RNA structural motif clustering using graph isomorphism network.NAR genomics and bioinformatics · 2025Article
- Article
- Novel biallelic TK2 mutations cause mitochondrial DNA depletion syndrome with infantile early-onset lipid storage myopathy.Orphanet journal of rare diseases · 2025Article
- Resolving the Structure of a Guanine Quadruplex in TMPRSS2 Messenger RNA by Circular Dichroism and Molecular Modeling.Chemistry (Weinheim an der Bergstrasse, Germany) · 2024Article
- Machine learning-based prediction of DNA G-quadruplex folding topology with G4ShapePredictor.Scientific reports · 2024Article
- RNAMotifProfile: a graph-based approach to build RNA structural motif profiles.NAR genomics and bioinformatics · 2024Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
Sophisticated analysis and simplified visualization are crucial for understanding complicated structures of biomacromolecules. DSSR (Dissecting the Spatial Structure of RNA) is an integrated computational tool that has streamlined the analysis and annotation of 3D nucleic acid structures. The program creates schematic block representations in diverse styles that can be seamlessly integrated into PyMOL and complement its other popular visualization options. In addition to portraying individual base blocks, DSSR can draw Watson-Crick pairs as long blocks and highlight the minor-groove edges. Notably, DSSR can dramatically simplify the depiction of G-quadruplexes by automatically detecting G-tetrads and treating them as large square blocks. The DSSR-enabled innovative schematics with PyMOL are aesthetically pleasing and highly informative: the base identity, pairing geometry, stacking interactions, double-helical stems, and G-quadruplexes are immediately obvious. These features can be accessed via four interfaces: the command-line interface, the DSSR plugin for PyMOL, the web application, and the web application programming interface. The supplemental PDF serves as a practical guide, with complete and reproducible examples. Thus, even beginners or occasional users can get started quickly, especially via the web application at http://skmatic.x3dna.org.
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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.