ArticleBioinformatics (Oxford, England)2018
RINspector: a Cytoscape app for centrality analyses and DynaMine flexibility prediction.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
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- Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design.International journal of molecular sciences · 2022Article
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- Electrophysiological, Morphologic, and Transcriptomic Profiling of the Ogura-CMS, DGMS and Maintainer Broccoli Lines.Plants (Basel, Switzerland) · 2022Article
- Theta-Defensins to Counter COVID-19 as Furin Inhibitors:Computational and mathematical methods in medicine · 2022Article
- Hotspots for mutations in the SARS-CoV-2 spike glycoprotein: a correspondence analysis.Scientific reports · 2021Article
- Centrality Measures in Residue Interaction Networks to Highlight Amino Acids in Protein-Protein Binding.Frontiers in bioinformatics · 2021Article
- Design of an engineered ACE2 as a novel therapeutics against COVID-19.Journal of theoretical biology · 2020Article
- Identifying Synergistic Mechanisms of Multiple Ingredients in Shuangbai Tablets against Proteinuria by Virtual Screening and a Network Pharmacology Approach.Evidence-based complementary and alternative medicine : eCAM · 2020Article
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- Computational characterization of the binding mode between oncoprotein Ets-1 and DNA-repair enzymes.Proteins · 2018Article
- Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the β barrel in fatty acid binding proteins.BMC structural biology · 2018Article
- The Inclusion of Water Molecules in Residue Interaction Networks Identifies Additional Central Residues.Frontiers in molecular biosciences · 2018Article
- Comparing protein structures with RINspector automation in Cytoscape.F1000Research · 2018Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationProtein function is directly related to amino acid residue composition and the dynamics of these residues. Centrality analyses based on residue interaction networks permit to identify key residues in a protein that are important for its fold or function. Such central residues and their environment constitute suitable targets for mutagenesis experiments. Predicted flexibility and changes in flexibility upon mutation provide valuable additional information for the design of such experiments.
resultsWe combined centrality analyses with DynaMine flexibility predictions in a Cytoscape app called RINspector. The app performs centrality analyses and directly visualizes the results on a graph of predicted residue flexibility. In addition, the effect of mutations on local flexibility can be calculated. AVAILABILITY AND IMPLEMENTATION: The app is publicly available in the Cytoscape app store. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
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