通过《结构域百科全书》探索整个蛋白质宇宙的结构多样性

IF 44.7 1区 综合性期刊 Q1 MULTIDISCIPLINARY SCIENCES Science Pub Date : 2024-11-01 DOI:10.1126/science.adq4946
Andy M. Lau, Nicola Bordin, Shaun M. Kandathil, Ian Sillitoe, Vaishali P. Waman, Jude Wells, Christine A. Orengo, David T. Jones
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引用次数: 0

摘要

AlphaFold 蛋白结构数据库(AFDB)包含超过 2.14 亿个由结构域组成的预测蛋白质结构,结构域是在多种结构和功能环境中发现的独立折叠单元。识别结构域可以进行许多功能和进化分析,但由于数据规模庞大,识别结构域仍然具有挑战性。利用深度学习方法,我们对 AFDB 中的每个结构域进行了检测和分类,编写了《结构域百科全书》(The Encyclopedia of Domains)。我们检测到了近 3.65 亿个域,比序列方法检测到的域多 1 亿多个,涵盖 100 多万个类群。令人欣慰的是,77% 的非冗余结构域与已知超家族相似,大大扩展了其结构域空间的代表性。我们在超家族之间发现了 10,000 多种新的结构相互作用,并在折叠空间连续体中发现了数千种新的折叠。
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Exploring structural diversity across the protein universe with The Encyclopedia of Domains
The AlphaFold Protein Structure Database (AFDB) contains more than 214 million predicted protein structures composed of domains, which are independently folding units found in multiple structural and functional contexts. Identifying domains can enable many functional and evolutionary analyses but has remained challenging because of the sheer scale of the data. Using deep learning methods, we have detected and classified every domain in the AFDB, producing The Encyclopedia of Domains. We detected nearly 365 million domains, over 100 million more than can be found by sequence methods, covering more than 1 million taxa. Reassuringly, 77% of the nonredundant domains are similar to known superfamilies, greatly expanding representation of their domain space. We uncovered more than 10,000 new structural interactions between superfamilies and thousands of new folds across the fold space continuum.
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来源期刊
Science
Science 综合性期刊-综合性期刊
CiteScore
61.10
自引率
0.90%
发文量
0
审稿时长
2.1 months
期刊介绍: Science is a leading outlet for scientific news, commentary, and cutting-edge research. Through its print and online incarnations, Science reaches an estimated worldwide readership of more than one million. Science’s authorship is global too, and its articles consistently rank among the world's most cited research. Science serves as a forum for discussion of important issues related to the advancement of science by publishing material on which a consensus has been reached as well as including the presentation of minority or conflicting points of view. Accordingly, all articles published in Science—including editorials, news and comment, and book reviews—are signed and reflect the individual views of the authors and not official points of view adopted by AAAS or the institutions with which the authors are affiliated. Science seeks to publish those papers that are most influential in their fields or across fields and that will significantly advance scientific understanding. Selected papers should present novel and broadly important data, syntheses, or concepts. They should merit recognition by the wider scientific community and general public provided by publication in Science, beyond that provided by specialty journals. Science welcomes submissions from all fields of science and from any source. The editors are committed to the prompt evaluation and publication of submitted papers while upholding high standards that support reproducibility of published research. Science is published weekly; selected papers are published online ahead of print.
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