ArticleBioinformatics (Oxford, England)2023
RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Article
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- Stable loci and functional gene controlling pod shattering resistance across multiple environments under different genetic backgrounds in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Delivery of Multifunctional Microspheres via Intravesical Instillation for Bladder Carcinoma: Therapeutic Potential and Mechanistic Insights.Advanced healthcare materials · 2026Article
- Honokiol blocks tumor development and metastasis through mitochondrion-targeted effects.Cell death & disease · 2026Article
- Comprehensive Pan-Cancer Analysis Reveals RNF20 as a Candidate Prognostic and Diagnostic Biomarker.Bioinformatics and biology insights · 2026Article
- Investigating the molecular mechanisms of the "Tianma-Gouteng" herb pair in treating Parkinson's disease: a bioinformatics approach and density functional theory with molecular dynamics simulations validation.Frontiers in bioinformatics · 2026Article
- Molecular mechanism of bisphenol A in promoting esophageal carcinoma based on network toxicology and molecular docking.Medicine · 2025Article
- Naringenin inhibits ferroptosis to reduce radiation-induced lung injury: insights from network Pharmacology and molecular docking.Pharmaceutical biology · 2025Article
- NtCML19 Is Recruited by Tobacco to Interact With the Deacetylase Protein RsDN3377 of Rhizoctonia solani AG3-TB, Inhibiting Fungal Infection.Molecular plant pathology · 2025Article
- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
- Homologous recombination and evolutionary arms race drive the adaptive evolution of African swine fever virus.Veterinary research · 2025Article
- Article
- GerAB residues predicted to interfere with water passage based on steered molecular dynamics are key to germinosome functionality.Frontiers in microbiology · 2025Article
- Using residue interaction networks to understand protein function and evolution and to engineer new proteins.Current opinion in structural biology · 2024Review
- N-acetyltransferase 10 affects the proliferation of intrahepatic cholangiocarcinoma and M2-type polarization of macrophages by regulating C-C motif chemokine ligand 2.Journal of translational medicine · 2024Article
- EsigPBP3 Was the Important Pheromone-Binding Protein to Recognize Male Pheromones and Key Eucalyptus Volatiles.International journal of molecular sciences · 2024Article
- Key interaction networks: Identifying evolutionarily conserved non-covalent interaction networks across protein families.Protein science : a publication of the Protein Society · 2024Article
- Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships.Physical chemistry chemical physics : PCCP · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RING-PyMOL is a plugin for PyMOL providing a set of analysis tools for structural ensembles and molecular dynamic simulations. RING-PyMOL combines residue interaction networks, as provided by the RING software, with structural clustering to enhance the analysis and visualization of the conformational complexity. It combines precise calculation of non-covalent interactions with the power of PyMOL to manipulate and visualize protein structures. The plugin identifies and highlights correlating contacts and interaction patterns that can explain structural allostery, active sites, and structural heterogeneity connected with molecular function. It is easy to use and extremely fast, processing and rendering hundreds of models and long trajectories in seconds. RING-PyMOL generates a number of interactive plots and output files for use with external tools. The underlying RING software has been improved extensively. It is 10 times faster, can process mmCIF files and it identifies typed interactions also for nucleic acids. AVAILABILITY AND IMPLEMENTATION: https://github.com/BioComputingUP/ring-pymol.
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