ArticleF1000Research2018
Comparing protein structures with RINspector automation in Cytoscape.
Article in F1000Research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Localized Rigidification and Allosteric Modulation Mechanisms of SARS-CoV-2 Spike Neutralization by Class 3 and Class 4 Antibodies at Atomic Resolution: An Integrated Computational Study of Binding, Dynamics, and Allostery.bioRxiv : the preprint server for biology · 2026Article
- 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
- Design, construction and in vivo functional assessment of a hinge truncated sFLT01.Gene therapy · 2023Article
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- Computer Simulations and Network-Based Profiling of Binding and Allosteric Interactions of SARS-CoV-2 Spike Variant Complexes and the Host Receptor: Dissecting the Mechanistic Effects of the Delta and Omicron Mutations.International journal of molecular sciences · 2022Article
- SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations.Journal of chemical information and modeling · 2022Article
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- Highlighted role of VEGFA in follow up of celiac disease.Gastroenterology and hepatology from bed to bench · 2019Article
- Evaluation of gene expression change in eosinophilic gastroenteritis.Gastroenterology and hepatology from bed to bench · 2019Article
- The Inclusion of Water Molecules in Residue Interaction Networks Identifies Additional Central Residues.Frontiers in molecular biosciences · 2018Article
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3 authors.
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Abstract
Residue interaction networks (RINs) have been shown to be relevant representations of the tertiary or quaternary structures of proteins, in particular thanks to network centrality analyses. We recently developed the RINspector 1.0.0 Cytoscape app, which couples centrality analyses with backbone flexibility predictions. This combined approach permits the identification of crucial residues for the folding or function of the protein that can constitute good targets for mutagenesis experiments. Here we present an application programming interface (API) for RINspector 1.1.0 that enables interplay between Cytoscape, RINspector and external languages, such as R or Python. This API provides easy access to batch centrality calculations and flexibility predictions, and allows for the easy comparison of results between different structures. These comparisons can lead to the identification of specific and conserved central residues, and show the impact of mutations to these and other residues on the flexibility of the proteins. We give two use cases to demonstrate the interest of these functionalities and provide the corresponding scripts: the first concerns NMR conformers, the second focuses on mutations in a structure.
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