Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
Acta Crystallogr D Struct Biol. 2021 Jan 1;77(Pt 1):28-40. doi: 10.1107/S2059798320014473.
Comparison of homologous structure models is a key step in analyzing protein structure. With a wealth of homologous structures, comparison becomes a tedious process, and often only a small (user-biased) selection of data is used. A multitude of structural superposition algorithms are then typically used to visualize the structures together in 3D and to compare them. Here, the Local Annotation of Homology-Matched Amino acids (LAHMA) website (https://lahma.pdb-redo.eu) is presented, which compares any structure model with all of its close homologs from the PDB-REDO databank. LAHMA displays structural features in sequence space, allowing users to uncover differences between homologous structure models that can be analyzed for their relevance to chemistry or biology. LAHMA visualizes numerous structural features, also allowing one-click comparison of structure-quality plots (for example the Ramachandran plot) and `in-browser' structural visualization of 3D models.
同源结构模型的比较是分析蛋白质结构的关键步骤。由于具有丰富的同源结构，比较成为一个繁琐的过程，通常只使用一小部分（用户偏好的）数据。然后，通常会使用多种结构叠加算法将结构一起以 3D 形式可视化，并进行比较。这里介绍了同源匹配氨基酸的局部注释（LAHMA）网站（https://lahma.pdb-redo.eu），它可以将任何结构模型与其来自 PDB-REDO 数据库的所有近同源物进行比较。LAHMA 在序列空间中显示结构特征，使用户能够发现同源结构模型之间的差异，从而可以分析这些差异与化学或生物学的相关性。LAHMA 可视化了许多结构特征，还允许一键比较结构质量图（例如 Ramachandran 图），并在浏览器中对 3D 模型进行结构可视化。
