SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning.
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning.
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SCOPe：蛋白质结构分类的改进-扩展数据库，以促进变体解释和机器学习。
DOI：
10.1093/nar/gkab1054
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发表时间：
2022-01-07
影响因子：
14.9
通讯作者：
Brenner SE
中科院分区：
文献类型：
--
作者：
Chandonia JM;Guan L;Lin S;Yu C;Fox NK;Brenner SE
扩展的蛋白质结构分类（SCOPe，https://scop.berkeley.edu）知识库旨在提供已知结构的大多数蛋白质之间的结构和进化关系的准确、详细和全面的描述，沿着用于分析蛋白质结构及其序列的资源。PDB中的结构被划分为多个域，并使用手动管理和高度精确的自动化方法进行分类。在当前发布的SCOPe，2.08中，我们开发了搜索和显示工具，用于分析我们映射到SCOPe中分类的结构的遗传变异。为了提高SCOPe在自动化方法中的实用性，例如依赖于同源蛋白质序列的多重比对的深度学习分类器，我们引入了新的机器可解析注释，这些注释指示异常结构以及由较小重复单元区分的结构域。我们还对来自74个以前未在SCOPe中分类的最大Pfam家族的结构进行了分类，并改进了我们的算法，以从SCOPe结构域中删除N-和C-末端克隆、表达和纯化序列。SCOPe 2.08-stable对106976个PDB条目进行了分类（约占PDB条目的60%）。
The Structural Classification of Proteins—extended (SCOPe, https://scop.berkeley.edu) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst the majority of proteins of known structure, along with resources for analyzing the protein structures and their sequences. Structures from the PDB are divided into domains and classified using a combination of manual curation and highly precise automated methods. In the current release of SCOPe, 2.08, we have developed search and display tools for analysis of genetic variants we mapped to structures classified in SCOPe. In order to improve the utility of SCOPe to automated methods such as deep learning classifiers that rely on multiple alignment of sequences of homologous proteins, we have introduced new machine-parseable annotations that indicate aberrant structures as well as domains that are distinguished by a smaller repeat unit. We also classified structures from 74 of the largest Pfam families not previously classified in SCOPe, and we improved our algorithm to remove N- and C-terminal cloning, expression and purification sequences from SCOPe domains. SCOPe 2.08-stable classifies 106 976 PDB entries (about 60% of PDB entries).
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影响因子：
14.9
作者：
Sillitoe I;Bordin N;Dawson N;Waman VP;Ashford P;Scholes HM;Pang CSM;Woodridge L;Rauer C;Sen N;Abbasian M;Le Cornu S;Lam SD;Berka K;Varekova IH;Svobodova R;Lees J;Orengo CA
通讯作者：
Orengo CA
影响因子：
14.9
作者：
Mistry J;Chuguransky S;Williams L;Qureshi M;Salazar GA;Sonnhammer ELL;Tosatto SCE;Paladin L;Raj S;Richardson LJ;Finn RD;Bateman A
通讯作者：
Bateman A
影响因子：
12.3
作者：
McLaren W;Gil L;Hunt SE;Riat HS;Ritchie GR;Thormann A;Flicek P;Cunningham F
通讯作者：
Cunningham F
影响因子：
64.8
作者：
Jumper J;Evans R;Pritzel A;Green T;Figurnov M;Ronneberger O;Tunyasuvunakool K;Bates R;Žídek A;Potapenko A;Bridgland A;Meyer C;Kohl SAA;Ballard AJ;Cowie A;Romera-Paredes B;Nikolov S;Jain R;Adler J;Back T;Petersen S;Reiman D;Clancy E;Zielinski M;Steinegger M;Pacholska M;Berghammer T;Bodenstein S;Silver D;Vinyals O;Senior AW;Kavukcuoglu K;Kohli P;Hassabis D
通讯作者：
Hassabis D
影响因子：
14.9
作者：
Chandonia, JM;Walker, NS;Brenner, SE
通讯作者：
Brenner, SE