ArticleNucleic acids research2024
RING 4.0: faster residue interaction networks with novel interaction types across over 35,000 different chemical structures.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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64 citing papers in PubMed.
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- Exploring proteins and protein-ligand complexes through residue interaction networks.Nature protocols · 2026Review
- Monoallelic POLR3A Variants Cause Early-Onset Peripheral Neuropathy.Annals of neurology · 2026Article
- State-dependent binding of the wedge domain controls inactivation of the mechanosensitive ion channel PIEZO1.Nature communications · 2026Article
- Virtual Screening of Bacteriocins From Lactic Acid Bacteria Against Monkeypox DNA Polymerase: Sakacin P and Mundticin KS Emerge as Promising Candidates.Food science & nutrition · 2026Article
- i-gRINN: a next-generation web server for protein energy network analysis of heterogeneous biomolecular systems with natural language-based data exploration.Nucleic acids research · 2026Article
- Structural Features of a Tiny Viral Protein, ORF7b of SARS-CoV-2.International journal of molecular sciences · 2026Article
- Conserved Active Site Loop Residues of E. coli DinB and Human DNA Polymerase Kappa Govern Activity.Environmental and molecular mutagenesis · 2026Article
- Molecular determinants of TNFR1:TNFα binding and dynamics in a physiological membrane environment.Current research in structural biology · 2026Article
- Thermostable ancestors enabled evolutionary diversification of promiscuous chemical defence enzymes.The EMBO journal · 2026Article
- Dopamine D2 Receptor Isoform Heteroreceptor Complexes with the Growth Hormone Secretagogue Receptor 1a Reveals Isoform-Specific Interaction Interface Dynamics.Journal of chemical information and modeling · 2026Article
- Toward a unified framework for determining conformational ensembles of disordered proteins.Nature methods · 2026Review
- Structural basis of human γTuRC closure during CM1-activated microtubule nucleation.Nature communications · 2026Article
- Article
- Honokiol blocks tumor development and metastasis through mitochondrion-targeted effects.Cell death & disease · 2026Article
- Cryo-EM structure of the vaccinia virus entry fusion complex reveals a multicomponent fusion machinery.Science advances · 2026Article
- G34R cancer mutation alters the conformational ensemble and dynamics of the histone H3.3 tails.Nucleic acids research · 2026Article
4 more citing papers are in PubMed but not listed here.
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8 authors.
Funding
Abstract
Residue interaction networks (RINs) are a valuable approach for representing contacts in protein structures. RINs have been widely used in various research areas, including the analysis of mutation effects, domain-domain communication, catalytic activity, and molecular dynamics simulations. The RING server is a powerful tool to calculate non-covalent molecular interactions based on geometrical parameters, providing high-quality and reliable results. Here, we introduce RING 4.0, which includes significant enhancements for identifying both covalent and non-covalent bonds in protein structures. It now encompasses seven different interaction types, with the addition of π-hydrogen, halogen bonds and metal ion coordination sites. The definitions of all available bond types have also been refined and RING can now process the complete PDB chemical component dictionary (over 35000 different molecules) which provides atom names and covalent connectivity information for all known ligands. Optimization of the software has improved execution time by an order of magnitude. The RING web server has been redesigned to provide a more engaging and interactive user experience, incorporating new visualization tools. Users can now visualize all types of interactions simultaneously in the structure viewer and network component. The web server, including extensive help and tutorials, is available from URL: https://ring.biocomputingup.it/.
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