Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA and Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
Nucleic Acids Res. 2014 Jan;42(Database issue):D304-9. doi: 10.1093/nar/gkt1240. Epub 2013 Dec 3.
Structural Classification of Proteins-extended (SCOPe, http://scop.berkeley.edu) is a database of protein structural relationships that extends the SCOP database. SCOP is a manually curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. Development of the SCOP 1.x series concluded with SCOP 1.75. The ASTRAL compendium provides several databases and tools to aid in the analysis of the protein structures classified in SCOP, particularly through the use of their sequences. SCOPe extends version 1.75 of the SCOP database, using automated curation methods to classify many structures released since SCOP 1.75. We have rigorously benchmarked our automated methods to ensure that they are as accurate as manual curation, though there are many proteins to which our methods cannot be applied. SCOPe is also partially manually curated to correct some errors in SCOP. SCOPe aims to be backward compatible with SCOP, providing the same parseable files and a history of changes between all stable SCOP and SCOPe releases. SCOPe also incorporates and updates the ASTRAL database. The latest release of SCOPe, 2.03, contains 59 514 Protein Data Bank (PDB) entries, increasing the number of structures classified in SCOP by 55% and including more than 65% of the protein structures in the PDB.
蛋白质结构分类扩展（SCOPe，http://scop.berkeley.edu）是一个蛋白质结构关系数据库，扩展了 SCOP 数据库。SCOP 是一个手动整理的数据库，根据结构和进化关系，按照层次结构对大多数已知结构的蛋白质的结构域进行排序。SCOP 1.x 系列的开发随着 SCOP 1.75 的发布而结束。ASTRAL 概览提供了几个数据库和工具来帮助分析 SCOP 分类的蛋白质结构，特别是通过使用它们的序列。SCOPe 扩展了 SCOP 数据库的 1.75 版，使用自动化的编目方法对 SCOP 1.75 发布以来发布的许多结构进行分类。我们已经严格地对我们的自动化方法进行了基准测试，以确保它们与手动编目一样准确，尽管有许多蛋白质我们的方法无法应用。SCOPe 也部分手动编目，以纠正 SCOP 中的一些错误。SCOPe 的目标是与 SCOP 向后兼容，提供相同的可解析文件，并在所有稳定的 SCOP 和 SCOPe 版本之间提供更改历史记录。SCOPe 还整合并更新了 ASTRAL 数据库。最新版本的 SCOPe，2.03，包含 59514 个蛋白质数据库（PDB）条目，将 SCOP 分类的结构数量增加了 55%，并包含了 PDB 中超过 65%的蛋白质结构。
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