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Updated: Jul 16, 2025
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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
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Rinmaker: a fast, versatile and reliable tool to determine residue interaction networks in proteins.
Alvise Spanò1, Lorenzo Fanton1, Davide Pizzolato1
1Department of Environmental Science, Computer Science and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Venice, Italy.
BMC Bioinformatics
|September 11, 2023
Summary
RINmaker is a new bioinformatics tool that generates Residue Interaction Networks (RINs) from protein structures. This software provides insights into protein topology and function, aiding biological research.
Area of Science:
- Bioinformatics
- Structural Biology
- Computational Biology
Background:
- Residue Interaction Networks (RINs) represent protein structures as graphs, simplifying complex 3D data.
- RINs aid in understanding the topological properties and biological functions of large proteins.
Purpose of the Study:
- Introduce RINmaker, a novel software for generating and visualizing RINs.
- Provide a fast, flexible, and powerful tool for RIN analysis.
Main Methods:
- RINmaker determines RINs including all standard non-covalent interactions.
- The software is available as open-source, cross-platform tool (command-line, web app, API).
Main Results:
- RINmaker demonstrates high efficiency and correctness through benchmarking against alternatives.
- The tool accurately generates and visualizes Residue Interaction Networks.
Conclusions:
- RINmaker is customizable for diverse applications, from experimental support to computational pipelines.
- Facilitates integration of data-driven approaches with physical models for protein analysis.
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