NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins

Sajjad Nematzadeh*, Nizamettin Aydin, Zeyneb Kurt, Mahsa Torkamanian-Afshar

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Interactions of RNA and DNA with proteins are crucial for elucidating intracellular processes in living organisms, diagnosing disorders, designing aptamer drugs, and other applications. Therefore, investigating the relationships between these macromolecules is essential to life science research. 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. NaProGraph utilizes a comprehensive and curated dataset encompassing nearly all interacting macromolecules in the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB). 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. Furthermore, the functional similarity of proteins can be inferred using protein families and clans from Pfam. The tool we have developed is publicly available at https://naprolink.com/NaProGraph/ background: Interactions between RNA and DNA with proteins are crucial for elucidating intracellular processes in living organisms, diagnosing disorders, designing aptamer drugs, and other applications. Therefore, investigating the relationships between these macromolecules is essential to life science research. method: 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. NaProGraph utilizes a comprehensive and curated dataset encompassing nearly all interacting macromolecules in the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB). 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 NAs and the similarity of the macromolecules' primary structures. Furthermore, the functional similarity of proteins can be inferred using protein families and clans from Pfam. conclusion: The NaProGraph tool serves as an effective online resource for researchers interested in studying interactions between nucleic acids and proteins. By leveraging a comprehensive dataset and providing various visualization and extraction capabilities, NaProGraph facilitates the exploration of macromolecular relationships and aids in understanding intracellular processes in living organisms. other: -
Original languageEnglish
Pages (from-to)385-397
Number of pages13
JournalCurrent Bioinformatics
Volume19
Issue number4
Early online date20 Oct 2023
DOIs
Publication statusPublished - 1 May 2024

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