nematzadeh, S. orcid.org/0000-0001-5064-2181, Aydin, N., Kurt, Z. orcid.org/0000-0003-3186-8091 et al. (1 more author) (2023) NaProGraph: Network analyzer for interactions between nucleic acids and proteins. Current Bioinformatics, 19 (4). pp. 385-397. ISSN 1574-8936
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.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2023 Bentham Science Publishers |
Keywords: | Interaction Network; RNA-protein; DNA-protein; NA-protein; online bioinformatics tool |
Dates: |
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Institution: | The University of Sheffield |
Academic Units: | The University of Sheffield > Faculty of Social Sciences (Sheffield) > Information School (Sheffield) |
Depositing User: | Symplectic Sheffield |
Date Deposited: | 23 Nov 2023 08:37 |
Last Modified: | 25 Oct 2024 15:40 |
Status: | Published |
Publisher: | Bentham Science Publishers Ltd. |
Refereed: | Yes |
Identification Number: | 10.2174/0115748936266189231004110412 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:205563 |