Suppr超能文献

揭开病毒信息学的网络:病毒研究中的计算工具和数据库

Unraveling the web of viroinformatics: computational tools and databases in virus research.

作者信息

Sharma Deepak, Priyadarshini Pragya, Vrati Sudhanshu

机构信息

Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Gurgaon, India

Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, Gurgaon, India.

出版信息

J Virol. 2015 Feb;89(3):1489-501. doi: 10.1128/JVI.02027-14. Epub 2014 Nov 26.

Abstract

The beginning of the second century of research in the field of virology (the first virus was discovered in 1898) was marked by its amalgamation with bioinformatics, resulting in the birth of a new domain--viroinformatics. The availability of more than 100 Web servers and databases embracing all or specific viruses (for example, dengue virus, influenza virus, hepatitis virus, human immunodeficiency virus [HIV], hemorrhagic fever virus [HFV], human papillomavirus [HPV], West Nile virus, etc.) as well as distinct applications (comparative/diversity analysis, viral recombination, small interfering RNA [siRNA]/short hairpin RNA [shRNA]/microRNA [miRNA] studies, RNA folding, protein-protein interaction, structural analysis, and phylotyping and genotyping) will definitely aid the development of effective drugs and vaccines. However, information about their access and utility is not available at any single source or on any single platform. Therefore, a compendium of various computational tools and resources dedicated specifically to virology is presented in this article.

摘要

病毒学领域研究进入第二个世纪(1898年发现了第一种病毒),其标志是与生物信息学融合,从而诞生了一个新领域——病毒信息学。有100多个涵盖所有或特定病毒(如登革热病毒、流感病毒、肝炎病毒、人类免疫缺陷病毒[HIV]、出血热病毒[HFV]、人乳头瘤病毒[HPV]、西尼罗河病毒等)的网络服务器和数据库,以及不同的应用程序(比较/多样性分析、病毒重组、小干扰RNA[siRNA]/短发夹RNA[shRNA]/微小RNA[miRNA]研究、RNA折叠、蛋白质-蛋白质相互作用、结构分析以及系统分型和基因分型),这无疑将有助于开发有效的药物和疫苗。然而,关于这些资源的访问方式和用途,在任何单一来源或平台上都无法获取。因此,本文介绍了专门针对病毒学的各种计算工具和资源的汇编。

相似文献

1
Unraveling the web of viroinformatics: computational tools and databases in virus research.
J Virol. 2015 Feb;89(3):1489-501. doi: 10.1128/JVI.02027-14. Epub 2014 Nov 26.
2
A new era of virus bioinformatics.
Virus Res. 2018 Jun 2;251:86-90. doi: 10.1016/j.virusres.2018.05.009. Epub 2018 May 8.
4
Computational tools to study and understand the intricate biology of mycobacteria.
Tuberculosis (Edinb). 2011 May;91(3):273-6. doi: 10.1016/j.tube.2011.02.005. Epub 2011 Mar 12.
5
Software Dedicated to Virus Sequence Analysis "Bioinformatics Goes Viral".
Adv Virus Res. 2017;99:233-257. doi: 10.1016/bs.aivir.2017.08.004. Epub 2017 Sep 28.
6
VIPERdb: A Tool for Virus Research.
Annu Rev Virol. 2018 Sep 29;5(1):477-488. doi: 10.1146/annurev-virology-092917-043405.
7
DengueInfo: A web portal to dengue information resources.
Infect Genet Evol. 2007 Jul;7(4):540-1. doi: 10.1016/j.meegid.2007.02.002. Epub 2007 Feb 11.
8
A survey of the availability of primary bioinformatics web resources.
Genomics Proteomics Bioinformatics. 2007 Feb;5(1):70-6. doi: 10.1016/S1672-0229(07)60017-5.
9
Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus.
BMC Bioinformatics. 2006 Dec 18;7 Suppl 5(Suppl 5):S4. doi: 10.1186/1471-2105-7-S5-S4.
10
The Bioinformatics Links Directory: a compilation of molecular biology web servers.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W3-24. doi: 10.1093/nar/gki594.

引用本文的文献

1
VITALdb: to select the best viroinformatics tools for a desired virus or application.
Brief Bioinform. 2025 Mar 4;26(2). doi: 10.1093/bib/bbaf084.
2
Bioinformatic Approaches for Comparative Analysis of Viruses.
Methods Mol Biol. 2024;2802:395-425. doi: 10.1007/978-1-0716-3838-5_13.
3
Navigating the Landscape: A Comprehensive Review of Current Virus Databases.
Viruses. 2023 Aug 29;15(9):1834. doi: 10.3390/v15091834.
5
Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.
Microorganisms. 2022 Nov 24;10(12):2327. doi: 10.3390/microorganisms10122327.
6
Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants.
Colloids Surf B Biointerfaces. 2023 Jan;221:112986. doi: 10.1016/j.colsurfb.2022.112986. Epub 2022 Oct 29.
7
The Landscape of Virus-Host Protein-Protein Interaction Databases.
Front Microbiol. 2022 Jul 15;13:827742. doi: 10.3389/fmicb.2022.827742. eCollection 2022.
8
The International Virus Bioinformatics Meeting 2022.
Viruses. 2022 May 5;14(5):973. doi: 10.3390/v14050973.
9
Up State of the SARS-COV-2 Spike Homotrimer Favors an Increased Virulence for New Variants.
Front Med Technol. 2021 Jun 30;3:694347. doi: 10.3389/fmedt.2021.694347. eCollection 2021.
10
VGEA: an RNA viral assembly toolkit.
PeerJ. 2021 Sep 6;9:e12129. doi: 10.7717/peerj.12129. eCollection 2021.

本文引用的文献

2
VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations.
Bioinformatics. 2014 Feb 15;30(4):578-80. doi: 10.1093/bioinformatics/btt724. Epub 2013 Dec 12.
3
VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses.
J Transl Med. 2013 Dec 11;11:305. doi: 10.1186/1479-5876-11-305.
4
AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses.
Nucleic Acids Res. 2014 Jan;42(Database issue):D1147-53. doi: 10.1093/nar/gkt1191. Epub 2013 Nov 26.
5
Viral IRES prediction system - a web server for prediction of the IRES secondary structure in silico.
PLoS One. 2013 Nov 5;8(11):e79288. doi: 10.1371/journal.pone.0079288. eCollection 2013.
6
bNAber: database of broadly neutralizing HIV antibodies.
Nucleic Acids Res. 2014 Jan;42(Database issue):D1133-9. doi: 10.1093/nar/gkt1083. Epub 2013 Nov 7.
7
Identification of novel viruses using VirusHunter--an automated data analysis pipeline.
PLoS One. 2013 Oct 22;8(10):e78470. doi: 10.1371/journal.pone.0078470. eCollection 2013.
9
HIV N-linked glycosylation site analyzer and its further usage in anchored alignment.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W454-8. doi: 10.1093/nar/gkt472. Epub 2013 Jun 8.
10
Bringing it all together: big data and HIV research.
AIDS. 2013 Mar 13;27(5):835-8. doi: 10.1097/QAD.0b013e32835cb785.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验