NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins

Background 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.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. NaProGraph utilizes a comprehensive and curated dataset encompassing nearly all interacting macromolecules 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.

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Son Erişim Tarihi
16 Temmuz 2024 17:07
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Eser Adı
(dc.title)
NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins
Yazar
(dc.contributor.author)
Sajjad Nematzadeh
Yayın Yılı
(dc.date.issued)
2024
Tür
(dc.type)
Makale
Özet
(dc.description.abstract)
Background 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.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. NaProGraph utilizes a comprehensive and curated dataset encompassing nearly all interacting macromolecules 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.
Açık Erişim Tarihi
(dc.date.available)
2030-08-27
Yayıncı
(dc.publisher)
BENTHAM SCIENCE PUBL LTD
Dil
(dc.language.iso)
En
Konu Başlıkları
(dc.subject)
Interaction network
Konu Başlıkları
(dc.subject)
RNA protein
Konu Başlıkları
(dc.subject)
DNA protein
Konu Başlıkları
(dc.subject)
NA protein
Konu Başlıkları
(dc.subject)
online bioinformatics tool
Konu Başlıkları
(dc.subject)
intracellular
Tek Biçim Adres
(dc.identifier.uri)
https://hdl.handle.net/20.500.14081/2113
ISSN
(dc.identifier.issn)
1574-8936
Dergi
(dc.relation.journal)
CURR BIOINFORM
Dergi Sayısı
(dc.identifier.issue)
4
Esere Katkı Sağlayan
(dc.contributor.other)
Nematzadeh, Sajjad
Esere Katkı Sağlayan
(dc.contributor.other)
Aydin, Nizamettin
Esere Katkı Sağlayan
(dc.contributor.other)
Kurt, Zeyneb
Esere Katkı Sağlayan
(dc.contributor.other)
Torkamanian-Afshar, Mahsa
DOI
(dc.identifier.doi)
10.2174/0115748936266189231004110412
Orcid
(dc.identifier.orcid)
0000-0001-5064-2181
Bitiş Sayfası
(dc.identifier.endpage)
397
Başlangıç Sayfası
(dc.identifier.startpage)
385
Dergi Cilt
(dc.identifier.volume)
19
wosquality
(dc.identifier.wosquality)
Q2
Department
(dc.contributor.department)
Yazılım Mühendisliği
Wos No
(dc.identifier.wos)
WOS:001255298500004
Veritabanları
(dc.source.platform)
Wos
Veritabanları
(dc.source.platform)
Scopus
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