Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures.
Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures.
复制标题
超越 US-SOMO-AF 数据库：一个新网站，用于对用户提供的结构进行流体动力学、结构和圆二色性计算。
DOI：
10.1007/s00249-023-01636-1
复制
发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Rocco,Mattia
中科院分区：
文献类型：
--
作者：
Brookes,EmreH;Rocco,Mattia
在第 25 届国际分析超速离心研讨会和研讨会上，我们描述了 UltraScan SOlution MOdeler AlphaFold (US-SOMO-AF) 数据库的最新实施情况，该数据库包含流体动力学、结构、CD 计算和其他辅助信息，在预测蛋白质结构的整个 AF v2 数据库（包含超过 1,000,000 个条目）上进行。 US-SOMO-AF 数据库的范围是提供对预先计算的物理化学参数的直接访问，以便根据实验确定的对应参数进行快速评估，以测试预测的 AlphaFold 结构溶液的兼容性。与此同时，AlphaFold 联盟已将其预测结构数据库扩展至惊人的 2 亿个条目，使其在 US-SOMO-AF 数据库中的覆盖范围变得相当不切实际。因此，我们创建了 US-SOMO-Web 站点，允许在用户提供的 PDB 和 mmCIF 结构上快速计算 US-SOMO-AF 数据库中存在的所有属性，并允许直接处理最新的 AlphaFold 模型。描述了网站的主要功能，以及当前的限制和未来潜在的发展。
At the 25th International Analytical Ultracentrifugation Workshop and Symposium, we described the recent implementation of the UltraScan SOlution MOdeler AlphaFold (US-SOMO-AF) database, containing hydrodynamic, structural, CD calculations, and other ancillary information, performed on the entire AF v2 database of predicted protein structures, containing more than 1,000,000 entries. The scope of the US-SOMO-AF database was that of providing direct access to pre-calculated physicochemical parameters for rapid assessment against their experimentally determined counterparts to test the compatibility in solution of predicted AlphaFold structures. In the meantime, the AlphaFold consortium has extended its database of predicted structures to an astonishing > 200 million entries, making it quite impractical for their coverage in the US-SOMO-AF database. Therefore, we have created the US-SOMO-Web site, allowing the rapid calculations of all the properties, as present in the US-SOMO-AF database, on user-supplied PDB and mmCIF structures, as well as allowing direct processing of the latest AlphaFold models. Major features on the website are described, along with current limitations and potential future developments.