文献检索文档翻译深度研究
Suppr Zotero 插件Zotero 插件
邀请有礼套餐&价格历史记录

新学期，新优惠

限时优惠:9月1日-9月22日

30天高级会员仅需29元

1天体验卡首发特惠仅需5.99元

了解详情
不再提醒
插件&应用
Suppr Zotero 插件Zotero 插件浏览器插件Mac 客户端Windows 客户端微信小程序
高级版
套餐订阅购买积分包
AI 工具
文献检索文档翻译深度研究
关于我们
关于 Suppr公司介绍联系我们用户协议隐私条款
关注我们

Suppr 超能文献

核心技术专利：CN118964589B侵权必究
粤ICP备2023148730 号-1Suppr @ 2025

使用 Foldseek 进行快速准确的蛋白质结构搜索。

Fast and accurate protein structure search with Foldseek.

机构信息

Quantitative and Computational Biology Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.

School of Biological Sciences, Seoul National University, Seoul, South Korea.

出版信息

Nat Biotechnol. 2024 Feb;42(2):243-246. doi: 10.1038/s41587-023-01773-0. Epub 2023 May 8.

DOI:10.1038/s41587-023-01773-0
PMID:37156916
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10869269/
Abstract

As structure prediction methods are generating millions of publicly available protein structures, searching these databases is becoming a bottleneck. Foldseek aligns the structure of a query protein against a database by describing tertiary amino acid interactions within proteins as sequences over a structural alphabet. Foldseek decreases computation times by four to five orders of magnitude with 86%, 88% and 133% of the sensitivities of Dali, TM-align and CE, respectively.

摘要

随着结构预测方法生成数以百万计的公开可用蛋白质结构，对这些数据库的搜索成为了一个瓶颈。Foldseek 通过将蛋白质中的三级氨基酸相互作用描述为结构字母表上的序列，将查询蛋白质的结构与数据库进行对齐。与 Dali、TM-align 和 CE 相比，Foldseek 的计算时间分别减少了四到五个数量级，灵敏度分别为 86%、88%和 133%。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d797/10869269/d3b6150f054c/41587_2023_1773_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d797/10869269/c8c15b4f3530/41587_2023_1773_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d797/10869269/d3b6150f054c/41587_2023_1773_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d797/10869269/c8c15b4f3530/41587_2023_1773_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d797/10869269/d3b6150f054c/41587_2023_1773_Fig2_HTML.jpg

相似文献

[1]
Fast and accurate protein structure search with Foldseek.

Nat Biotechnol. 2024-2

[2]
TM-search: An Efficient and Effective Tool for Protein Structure Database Search.

J Chem Inf Model. 2024-2-12

[3]
Using Dali for structural comparison of proteins.

Curr Protoc Bioinformatics. 2006-7

[4]
Large-scale comparison of protein sequence alignment algorithms with structure alignments.

Proteins. 2000-7-1

[5]
mTM-align: a server for fast protein structure database search and multiple protein structure alignment.

Nucleic Acids Res. 2018-7-2

[6]
Protein structure mining using a structural alphabet.

Proteins. 2008-5-1

[7]
Searching protein structure databases with DaliLite v.3.

Bioinformatics. 2008-12-1

[8]
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score.

BMC Bioinformatics. 2008-12-12

[9]
TM-align: a protein structure alignment algorithm based on the TM-score.

Nucleic Acids Res. 2005-4-22

[10]
YAKUSA: a fast structural database scanning method.

Proteins. 2005-10-1

引用本文的文献

[1]
Escherichia coli strain O55 contains two cryptic plasmids that depend on each other to replicate.

Arch Microbiol. 2025-9-9

[2]
Design of a Multi-Epitope Vaccine using β-barrel Outer Membrane Proteins Identified in Chlamydia trachomatis.

J Membr Biol. 2025-9-4

[3]
Systematic functional assessment of anti-phage systems in their native host.

Philos Trans R Soc Lond B Biol Sci. 2025-9-4

[4]
Deciphering enzymatic potential in metagenomic reads through DNA language models.

Nucleic Acids Res. 2025-8-27

[5]
The discovery of a phage explains a key determinant of human disease.

Sci Adv. 2025-9-5

[6]
Functional (re)annotation of proteome using integrative sequence and AI-based structural approaches.

Curr Res Struct Biol. 2025-8-6

[7]
Structural basis for binding of RILPL1 to TMEM55B reveals a lysosomal platform for adaptor assembly through a conserved TBM motif.

bioRxiv. 2025-8-24

[8]
A prevalent huge phage clade in human and animal gut microbiomes.

Res Sq. 2025-8-19

[9]
A family of tubular pili from harmful algal bloom forming cyanobacterium Microcystis aeruginosa.

Nat Commun. 2025-8-29

[10]
Chemoenzymatic total synthesis of the antibiotic (-)-13-deoxytetrodecamycin using the Diels-Alderase TedJ.

Chem Sci. 2025-8-26

本文引用的文献

[1]
Foldcomp: a library and format for compressing and indexing large protein structure sets.

Bioinformatics. 2023-4-3

[2]
Evolutionary-scale prediction of atomic-level protein structure with a language model.

Science. 2023-3-17

[3]
AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms.

Commun Biol. 2023-2-8

[4]
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models.

Nucleic Acids Res. 2022-1-7

[5]
Accurate prediction of protein structures and interactions using a three-track neural network.

Science. 2021-8-20

[6]
Highly accurate protein structure prediction with AlphaFold.

Nature. 2021-8

[7]
Sensitive protein alignments at tree-of-life scale using DIAMOND.

Nat Methods. 2021-4

[8]
DeepAlign, a 3D alignment method based on regionalized deep learning for Cryo-EM.

J Struct Biol. 2021-6

[9]
Geometricus represents protein structures as shape-mers derived from moment invariants.

Bioinformatics. 2020-12-30

[10]
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.

Nucleic Acids Res. 2021-1-8

文献AI研究员

20分钟写一篇综述，助力文献阅读效率提升50倍

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

推荐工具

医学文档翻译智能文献检索