Guo Dongjun, Ng Joseph Chi-Fung, Dunn-Walters Deborah K, Fraternali Franca
Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom.
Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, United Kingdom.
Bioinform Adv. 2024 Sep 20;4(1):vbae137. doi: 10.1093/bioadv/vbae137. eCollection 2024.
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. 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.
The and region bearing ntiody (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.
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.
针对免疫挑战的有效反应需要具有不同同种型的抗体发挥特定的效应功能。这些同种型的结构信息对于构建具有所需抗原结合特性的物理化学特征以及作为潜在治疗药物的最佳可开发性的抗体至关重要。抗体结构上的突变扫描图谱将进一步确定增强抗体稳定性和功能的候选突变。当前的抗体结构数据库缺乏对同种型的一致注释、三维抗体结构的结构覆盖范围以及计算出的深度突变图谱。
建立了带有抗体可变区和恒定区（VCAb）的网络工具，以澄清这些注释，并提供一个便于使用的资源来促进抗体工程和设计。VCAb目前提供了7166个实验确定的抗体结构数据，包括来自不同物种的可变区和恒定区。此外，VCAb还提供了应用编号方案的物种和同种型注释。这些信息可以交互式查询或批量下载。
VCAb作为一个R shiny应用程序实现，以实现交互式数据查询。该在线应用程序可在https://fraternalilab.cs.ucl.ac.uk/VCAb/免费访问。生成数据库和在线应用程序的源代码在https://github.com/Fraternalilab/VCAb上开源提供。
