VCAb: a web-tool for structure-guided exploration of antibodies.

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
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引用次数: 0

Abstract

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.

VCAb:结构引导下的抗体探索网络工具。
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。
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CiteScore
1.60
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0.00%
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