Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
Department of Computer Science, Purdue University, West Lafayette, IN, USA.
Nat Commun. 2021 Apr 7;12(1):2090. doi: 10.1038/s41467-021-22401-y.
An increasing number of density maps of biological macromolecules have been determined by cryo-electron microscopy (cryo-EM) and stored in the public database, EMDB. To interpret the structural information contained in EM density maps, alignment of maps is an essential step for structure modeling, comparison of maps, and for database search. Here, we developed VESPER, which captures the similarity of underlying molecular structures embedded in density maps by taking local gradient directions into consideration. Compared to existing methods, VESPER achieved substantially more accurate global and local alignment of maps as well as database retrieval.
越来越多的生物大分子密度图已经通过冷冻电子显微镜（cryo-EM）确定，并存储在公共数据库 EMDB 中。为了解释 EM 密度图中包含的结构信息，图谱对齐是结构建模、图谱比较和数据库搜索的重要步骤。在这里，我们开发了 VESPER，它通过考虑密度图中嵌入的底层分子结构的局部梯度方向来捕捉相似性。与现有方法相比，VESPER 实现了更准确的全局和局部图谱对齐以及数据库检索。
