GAG Builder：一种用于建模糖胺聚糖 3D 结构的网络工具。
GAG Builder: a web-tool for modeling 3D structures of glycosaminoglycans.
机构信息
Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, USA.
出版信息
Glycobiology. 2019 Jul 1;29(7):515-518. doi: 10.1093/glycob/cwz027.
Abstract
Here we report the launch of a web-tool (the GLYCAM-Web GAG Builder, www.glycam.org/gag) for the rapid and straightforward prediction of 3D structural models for glycosaminoglycans (GAGs). The tool provides the user with coordinate files (PDB format) for use in visualization, as well as files for performing MD simulation with the AMBER software package. Counter ions and water may also be added as desired. The tool is designed with the non-expert in mind, and as such has implemented typical default values for structural parameters, which the user may change if desired. Multiple GAG types are supported, including Heparin/Heparan Sulfate, Chondroitin Sulfate, Dermatan Sulfate, Keratan Sulfate, and Hyaluronan; however, the user may alter the default sulfation patterns to create novel sequences. The common non-natural unsaturated uronic acid (ΔUA) and its sulfated derivative are also supported.
摘要
在这里，我们报告了一个网络工具（GLYCAM-Web GAG Builder，www.glycam.org/gag）的推出，该工具用于快速、直接地预测糖胺聚糖（GAG）的 3D 结构模型。该工具为用户提供坐标文件（PDB 格式），用于可视化，以及使用 AMBER 软件包进行 MD 模拟的文件。根据需要，还可以添加抗衡离子和水。该工具是为非专业人士设计的，因此为结构参数实现了典型的默认值，如果需要，用户可以更改这些默认值。该工具支持多种 GAG 类型，包括肝素/硫酸肝素、软骨素硫酸酯、硫酸皮肤素、硫酸角质素和透明质酸；但是，用户可以改变默认的硫酸化模式来创建新的序列。该工具还支持常见的非天然不饱和糖醛酸（ΔUA）及其硫酸化衍生物。
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