Grant Oliver C, Wentworth Daniel, Holmes Samuel G, Kandel Rajan, Sehnal David, Wang Xiaocong, Xiao Yao, Sheppard Preston, Grelsson Tobias, Coulter Andrew, Miller Grayson, Foley Bethany L, Woods Robert J
Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States.
National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic.
bioRxiv. 2025 May 9:2025.05.08.652828. doi: 10.1101/2025.05.08.652828.
The carbohydrate 3D structure-prediction tools (builders) at GLYCAM-Web (glycam.org) are widely used for generating experimentally-consistent 3D structures of oligosaccharides suitable for data interpretation, hypothesis generation, simple visualization, and subsequent molecular dynamics (MD) simulation. The graphical user interface (GUI) enables users to create carbohydrate sequences (e.g. DGalpb1-4DGlcpb1-OH) that are converted to 3D models of the carbohydrate structures in multiple formats, including PDB and OFF (AMBER software format). The resulting structures are energy minimized prior to download and online visualization. There are advanced options for selecting which shapes (rotamers) of the oligosaccharide to generate, and for creating explicitly solvated structures for subsequent MD simulation. The GLYCAM-Web builders integrate known conformational preferences of oligosaccharides, summarized here, and employ the GLYCAM forcefield for energy minimization with algorithms tailored for speed and scalability. Even for large oligosaccharides (100 residues, ~2100 atoms) a 3D structure is typically returned to the user in less than a minute.
GLYCAM-Web（glycam.org）上的碳水化合物三维结构预测工具（构建器）被广泛用于生成与实验结果一致的寡糖三维结构，适用于数据解释、假设生成、简单可视化以及后续的分子动力学（MD）模拟。图形用户界面（GUI）使用户能够创建碳水化合物序列（例如DGalpb1-4DGlcpb1-OH），这些序列会被转换为多种格式的碳水化合物结构三维模型，包括PDB和OFF（AMBER软件格式）。生成的结构在下载和在线可视化之前会进行能量最小化处理。有一些高级选项可用于选择生成寡糖的哪些形状（旋转异构体），以及创建用于后续MD模拟的明确溶剂化结构。GLYCAM-Web构建器整合了寡糖已知的构象偏好（在此进行了总结），并采用GLYCAM力场进行能量最小化，所使用的算法针对速度和可扩展性进行了优化。即使对于大型寡糖（100个残基，约2100个原子），通常也能在不到一分钟的时间内将三维结构返回给用户。
