NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins

IF 2.4 3区生物学 Q3 BIOCHEMICAL RESEARCH METHODS

Current Bioinformatics Pub Date : 2023-10-20 DOI:10.2174/0115748936266189231004110412

Sajjad nematzadeh, Nizamettin Aydin, Zeyneb Kurt, Mahsa Torkamanian-Afshar

{"title":"NaProGraph: Network Analyzer for Interactions between Nucleic Acids and Proteins","authors":"Sajjad nematzadeh, Nizamettin Aydin, Zeyneb Kurt, Mahsa Torkamanian-Afshar","doi":"10.2174/0115748936266189231004110412","DOIUrl":null,"url":null,"abstract":"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: -","PeriodicalId":10801,"journal":{"name":"Current Bioinformatics","volume":null,"pages":null},"PeriodicalIF":2.4000,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current Bioinformatics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.2174/0115748936266189231004110412","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}

引用次数: 0

Abstract

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: -

查看原文本刊更多论文

核酸与蛋白质相互作用的网络分析仪

RNA和DNA与蛋白质的相互作用对于阐明生物体的细胞内过程、诊断疾病、设计适体药物以及其他应用至关重要。因此，研究这些大分子之间的关系对生命科学研究至关重要。本研究提出了一个在线网络提供者工具(naprogram)，该工具提供了一个直观和用户友好的界面，用于研究核酸(NA)与蛋白质之间的相互作用。naprogram利用结构生物信息学研究合作实验室(RCSB)蛋白质数据库(PDB)中几乎所有相互作用的大分子的综合和精心策划的数据集。研究人员可以使用这个在线工具来关注PDB的特定部分，调查其相关关系，并可视化和提取相关信息。该工具提供了蛋白质和核酸(NAs)之间原子和残基的频率以及大分子初级结构的相似性的见解。此外，蛋白质的功能相似性可以通过Pfam的蛋白质家族和氏族来推断。我们开发的工具可在https://naprolink.com/NaProGraph/上公开获得。背景:RNA和DNA与蛋白质之间的相互作用对于阐明活生物体的细胞内过程、诊断疾病、设计适体药物和其他应用至关重要。因此，研究这些大分子之间的关系对生命科学研究至关重要。方法:本研究提出了一个在线网络提供者工具(NaProGraph)，该工具为研究核酸(NA)与蛋白质之间的相互作用提供了一个直观和用户友好的界面。naprogram利用结构生物信息学研究合作实验室(RCSB)蛋白质数据库(PDB)中几乎所有相互作用的大分子的综合和精心策划的数据集。研究人员可以使用这个在线工具来关注PDB的特定部分，调查其相关关系，并可视化和提取相关信息。该工具提供了蛋白质和NAs之间原子和残基的频率以及大分子初级结构的相似性的见解。此外，蛋白质的功能相似性可以通过Pfam的蛋白质家族和氏族来推断。结论:napgraph工具为研究核酸与蛋白质相互作用的研究人员提供了一个有效的在线资源。通过利用一个全面的数据集，提供各种可视化和提取功能，nagraph促进了大分子关系的探索，并有助于理解活生物体的细胞内过程。其他:-

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Current Bioinformatics 生物-生化研究方法

CiteScore

6.60

自引率

2.50%

发文量

审稿时长

>12 weeks

期刊介绍： Current Bioinformatics aims to publish all the latest and outstanding developments in bioinformatics. Each issue contains a series of timely, in-depth/mini-reviews, research papers and guest edited thematic issues written by leaders in the field, covering a wide range of the integration of biology with computer and information science. The journal focuses on advances in computational molecular/structural biology, encompassing areas such as computing in biomedicine and genomics, computational proteomics and systems biology, and metabolic pathway engineering. Developments in these fields have direct implications on key issues related to health care, medicine, genetic disorders, development of agricultural products, renewable energy, environmental protection, etc.