CSDB/SNFG Structure Editor: An Online Glycan Builder with 2D and 3D Structure Visualization,Journal of Chemical Information and Modeling

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CSDB/SNFG Structure Editor: An Online Glycan Builder with 2D and 3D Structure Visualization
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2021-10-01 , DOI: 10.1021/acs.jcim.1c00917
Andrei Y Bochkov ₁ , Philip V Toukach _{1,

2}

Affiliation

This article describes features, usage, and application of an CSDB/SNFG Structure Editor, a new online tool for quick and intuitive input of carbohydrate and derivative structures using Symbol Nomenclature for Glycans (SNFG). The Editor is built on a platform of the Carbohydrate Structure Database (CSDB) and relies on its online services via the dedicated web-API. The Editor allows building of oligo- and polymeric glycan structures and supports most features of natural glycans, such as underdetermined structures, alternative branches, repeating subunits, SMILES specification of atypical monomers, and others. The vocabulary of building blocks contains 600+ monomeric residues, including 327 monosaccharides. Support for SMILES allows input and visualization of chemical structures of virtually unlimited complexity. On the other hand, the interface follows the recognized GlycanBuilder style easy to novice users. The export feature includes support for CSDB Linear, GlycoCT, WURCS, SweetDB, and Glycam notations, SMILES codes, MOL/PDB atomic coordinate formats, raster and vector SNFG images, and on-the-fly visualization as 2D structural formulas and 3D molecular models. Integration of the Editor into any web-based glycoinformatics project is straightforward and simple, similarly to any other modern JavaScript application.

中文翻译：

CSDB/SNFG 结构编辑器：具有 2D 和 3D 结构可视化功能的在线聚糖生成器

本文介绍了 CSDB/SNFG 结构编辑器的功能、用法和应用，这是一种使用聚糖符号命名法 (SNFG) 快速直观地输入碳水化合物和衍生结构的新在线工具。编辑器建立在碳水化合物结构数据库 (CSDB) 的平台上，并通过专用的 Web-API 依赖其在线服务。编辑器允许构建寡聚糖和聚合聚糖结构，并支持天然聚糖的大多数特征，例如未确定结构、替代分支、重复亚基、非典型单体的 SMILES 规范等。积木词汇包含 600 多个单体残基，其中包括 327 个单糖。对 SMILES 的支持允许输入和可视化几乎无限复杂的化学结构。另一方面，界面遵循公认的 GlycanBuilder 风格，易于新手用户使用。导出功能包括支持 CSDB Linear、GlycoCT、WURCS、SweetDB 和 Glycam 符号、SMILES 代码、MOL/PDB 原子坐标格式、光栅和矢量 SNFG 图像，以及作为 2D 结构公式和 3D 分子模型的动态可视化. 与任何其他现代 JavaScript 应用程序类似，将编辑器集成到任何基于 Web 的糖信息学项目中都是直接而简单的。

更新日期：2021-10-25

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