VCAb:结构引导下的抗体探索网络工具。

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY
Bioinformatics advances Pub Date : 2024-09-20 eCollection Date: 2024-01-01 DOI:10.1093/bioadv/vbae137
Dongjun Guo, Joseph Chi-Fung Ng, Deborah K Dunn-Walters, Franca Fraternali
{"title":"VCAb:结构引导下的抗体探索网络工具。","authors":"Dongjun Guo, Joseph Chi-Fung Ng, Deborah K Dunn-Walters, Franca Fraternali","doi":"10.1093/bioadv/vbae137","DOIUrl":null,"url":null,"abstract":"<p><strong>Motivation: </strong>Effective responses against immune challenges require antibodies of different isotypes performing specific effector functions. Structural information on these isotypes is essential to engineer antibodies with desired physico-chemical features of their antigen-binding properties, and optimal developability as potential therapeutics. <i>In silico</i> mutational scanning profiles on antibody structures would further pinpoint candidate mutations for enhancing antibody stability and function. Current antibody structure databases lack consistent annotations of isotypes and structural coverage of 3D antibody structures, as well as computed deep mutation profiles.</p><p><strong>Results: </strong>The <i>V</i> and <i>C</i> region bearing <i>a</i>nti<i>b</i>ody (VCAb) web-tool is established to clarify these annotations and provides an accessible resource to facilitate antibody engineering and design. VCAb currently provides data on 7,166 experimentally determined antibody structures including both V and C regions from different species. Additionally, VCAb provides annotations of species and isotypes with numbering schemes applied. These information can be interactively queried or downloaded in batch.</p><p><strong>Availability and implementation: </strong>VCAb is implemented as a R shiny application to enable interactive data interrogation. The online application is freely accessible https://fraternalilab.cs.ucl.ac.uk/VCAb/. The source code to generate the database and the online application is available open-source at https://github.com/Fraternalilab/VCAb.</p>","PeriodicalId":72368,"journal":{"name":"Bioinformatics advances","volume":"4 1","pages":"vbae137"},"PeriodicalIF":2.4000,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11471263/pdf/","citationCount":"0","resultStr":"{\"title\":\"VCAb: a web-tool for structure-guided exploration of antibodies.\",\"authors\":\"Dongjun Guo, Joseph Chi-Fung Ng, Deborah K Dunn-Walters, Franca Fraternali\",\"doi\":\"10.1093/bioadv/vbae137\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Motivation: </strong>Effective responses against immune challenges require antibodies of different isotypes performing specific effector functions. Structural information on these isotypes is essential to engineer antibodies with desired physico-chemical features of their antigen-binding properties, and optimal developability as potential therapeutics. <i>In silico</i> mutational scanning profiles on antibody structures would further pinpoint candidate mutations for enhancing antibody stability and function. Current antibody structure databases lack consistent annotations of isotypes and structural coverage of 3D antibody structures, as well as computed deep mutation profiles.</p><p><strong>Results: </strong>The <i>V</i> and <i>C</i> region bearing <i>a</i>nti<i>b</i>ody (VCAb) web-tool is established to clarify these annotations and provides an accessible resource to facilitate antibody engineering and design. VCAb currently provides data on 7,166 experimentally determined antibody structures including both V and C regions from different species. Additionally, VCAb provides annotations of species and isotypes with numbering schemes applied. These information can be interactively queried or downloaded in batch.</p><p><strong>Availability and implementation: </strong>VCAb is implemented as a R shiny application to enable interactive data interrogation. The online application is freely accessible https://fraternalilab.cs.ucl.ac.uk/VCAb/. The source code to generate the database and the online application is available open-source at https://github.com/Fraternalilab/VCAb.</p>\",\"PeriodicalId\":72368,\"journal\":{\"name\":\"Bioinformatics advances\",\"volume\":\"4 1\",\"pages\":\"vbae137\"},\"PeriodicalIF\":2.4000,\"publicationDate\":\"2024-09-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11471263/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Bioinformatics advances\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1093/bioadv/vbae137\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q2\",\"JCRName\":\"MATHEMATICAL & COMPUTATIONAL BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Bioinformatics advances","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1093/bioadv/vbae137","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"MATHEMATICAL & COMPUTATIONAL BIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

动机针对免疫挑战的有效反应需要不同异型的抗体发挥特定的效应功能。要使抗体具有理想的抗原结合理化特性,并能作为潜在的治疗药物进行最佳开发,这些抗体异型的结构信息至关重要。对抗体结构进行硅学突变扫描可以进一步确定增强抗体稳定性和功能的候选突变。目前的抗体结构数据库缺乏一致的同种型注释和三维抗体结构的结构覆盖范围,也缺乏计算的深度突变图谱:结果:V和C区抗体(VCAb)网络工具的建立是为了澄清这些注释,并提供一个可访问的资源,以促进抗体工程和设计。VCAb 目前提供了 7,166 个实验确定的抗体结构数据,包括来自不同物种的 V 区和 C 区。此外,VCAb 还提供了物种和异型的注释,并应用了编号方案。这些信息可以交互式查询或批量下载:VCAb以R闪亮应用程序的形式实现,可进行交互式数据查询。该在线应用程序可免费访问 https://fraternalilab.cs.ucl.ac.uk/VCAb/。生成数据库和在线应用程序的源代码可在 https://github.com/Fraternalilab/VCAb 上免费获取。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
VCAb: a web-tool for structure-guided exploration of antibodies.

Motivation: Effective responses against immune challenges require antibodies of different isotypes performing specific effector functions. Structural information on these isotypes is essential to engineer antibodies with desired physico-chemical features of their antigen-binding properties, and optimal developability as potential therapeutics. In silico mutational scanning profiles on antibody structures would further pinpoint candidate mutations for enhancing antibody stability and function. Current antibody structure databases lack consistent annotations of isotypes and structural coverage of 3D antibody structures, as well as computed deep mutation profiles.

Results: The V and C region bearing antibody (VCAb) web-tool is established to clarify these annotations and provides an accessible resource to facilitate antibody engineering and design. VCAb currently provides data on 7,166 experimentally determined antibody structures including both V and C regions from different species. Additionally, VCAb provides annotations of species and isotypes with numbering schemes applied. These information can be interactively queried or downloaded in batch.

Availability and implementation: VCAb is implemented as a R shiny application to enable interactive data interrogation. The online application is freely accessible https://fraternalilab.cs.ucl.ac.uk/VCAb/. The source code to generate the database and the online application is available open-source at https://github.com/Fraternalilab/VCAb.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
CiteScore
1.60
自引率
0.00%
发文量
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信