NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins


Nematzadeh S., AYDIN N., Kurt Z., Torkamanian-Afshar M.

Current Bioinformatics, vol.19, no.4, pp.385-397, 2024 (SCI-Expanded) identifier

  • Publication Type: Article / Article
  • Volume: 19 Issue: 4
  • Publication Date: 2024
  • Doi Number: 10.2174/0115748936266189231004110412
  • Journal Name: Current Bioinformatics
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, Biotechnology Research Abstracts, Chemical Abstracts Core, EMBASE
  • Page Numbers: pp.385-397
  • Keywords: DNA protein, Interaction network, intracellular, NA protein, online bioinformatics tool, RNA protein
  • Yıldız Technical University Affiliated: Yes

Abstract

Background: Interactions of RNA and DNA with proteins are crucial for elucidating intra-cellular processes in living organisms, diagnosing disorders, designing aptamer drugs, and other ap-plications. Therefore, investigating the relationships between these macromolecules is essential to life science research. Methods: This study proposes an online network provider tool (NaProGraph) that offers an intuitive and user-friendly interface for studying interactions between nucleic acids (NA) and proteins. NaPro-Graph utilizes a comprehensive and curated dataset encompassing nearly all interacting macromole-cules in the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB). Results: Researchers can employ this online tool to focus on a specific portion of the PDB, investigate its associated relationships, and visualize and extract pertinent information. This tool provides insights into the frequency of atoms and residues between proteins and nucleic acids (NAs) and the similarity of the macromolecules' primary structures. Conclusion: Furthermore, the functional similarity of proteins can be inferred using protein families and clans from Pfam.