Abstract

VIrus Particle ExploreR data base (VIPERdb) (http://viperdb.scripps.edu) is a curated repository of virus capsid structures and a database of structure-derived data along with various virus specific information. VIPERdb has been continuously improved for over 20 years and contains a number of virus structure analysis tools. The release of VIPERdb v3.0 contains new structure-based data analytics tools like Multiple Structure-based and Sequence Alignment (MSSA) to identify hot-spot residues within a selected group of structures and an anomaly detection application to analyze and curate the structure-derived data within individual virus families. At the time of this writing, there are 931 virus structures from 62 different virus families in the database. Significantly, the new release also contains a standalone database called ‘Virus World database’ (VWdb) that comprises all the characterized viruses (∼181 000) known to date, gathered from ICTVdb and NCBI, and their capsid protein sequences, organized according to their virus taxonomy with links to known structures in VIPERdb and PDB. Moreover, the new release of VIPERdb includes a service-oriented data engine to handle all the data access requests and provides an interface for futuristic data analytics using machine leaning applications.

中文翻译：

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VIPERdb v3.0：基于结构的病毒衣壳数据分析平台

摘要

VIrus Particle Explorer 数据库 (VIPERdb) (http://viperdb.scripps.edu) 是病毒衣壳结构和结构衍生数据以及各种病毒特定信息的数据库。VIPERdb 经过 20 多年的不断改进，包含了许多病毒结构分析工具。VIPERdb v3.0 的发布包含新的基于结构的数据分析工具，例如基于多结构和序列比对 (MSSA)，用于识别选定结构组中的热点残基，以及用于分析和管理结构的异常检测应用程序 -单个病毒家族中的派生数据。在撰写本文时，数据库中有来自 62 个不同病毒家族的 931 个病毒结构。显着地，新版本还包含一个名为“病毒世界数据库”（VWdb）的独立数据库，该数据库包含迄今为止已知的所有特征病毒（~181 000），从 ICTVdb 和 NCBI 收集，及其衣壳蛋白序列，根据病毒分类组织与 VIPERdb 和 PDB 中已知结构的链接。此外，新版本的 VIPERdb 包括一个面向服务的数据引擎，用于处理所有数据访问请求，并为使用机器学习应用程序的未来数据分析提供接口。