• 文献检索
  • 文档翻译
  • 深度研究
  • 学术资讯
  • Suppr Zotero 插件Zotero 插件
  • 邀请有礼
  • 套餐&价格
  • 历史记录
应用&插件
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
定价
高级版会员购买积分包购买API积分包
服务
文献检索文档翻译深度研究API 文档MCP 服务
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 @ 2026

文献检索

告别复杂PubMed语法，用中文像聊天一样搜索，搜遍4000万医学文献。AI智能推荐，让科研检索更轻松。

立即免费搜索

文件翻译

保留排版，准确专业，支持PDF/Word/PPT等文件格式，支持 12+语言互译。

免费翻译文档

深度研究

AI帮你快速写综述，25分钟生成高质量综述，智能提取关键信息，辅助科研写作。

立即免费体验

TMBETA-GENOME：基因组序列中带注释的β-桶状膜蛋白数据库。

TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences.

作者信息

Gromiha M Michael, Yabuki Yukimitsu, Kundu Srinesh, Suharnan Sivasundaram, Suwa Makiko

机构信息

Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) AIST Tokyo Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan.

出版信息

Nucleic Acids Res. 2007 Jan;35(Database issue):D314-6. doi: 10.1093/nar/gkl805. Epub 2006 Nov 6.

DOI:10.1093/nar/gkl805
PMID:17088282
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1669718/
Abstract

We have developed the database, TMBETA-GENOME, for annotated beta-barrel membrane proteins in genomic sequences using statistical methods and machine learning algorithms. The statistical methods are based on amino acid composition, reside pair preference and motifs. In machine learning techniques, the combination of amino acid and dipeptide compositions has been used as main attributes. In addition, annotations have been made using the criterion based on the identification of beta-barrel membrane proteins and exclusion of globular and transmembrane helical proteins. A web interface has been developed for identifying the annotated beta-barrel membrane proteins in all known genomes. The users have the feasibility of selecting the genome from the three kingdoms of life, archaea, bacteria and eukaryote, and five different methods. Further, the statistics for all genomes have been provided along with the links to different algorithms and related databases. It is freely available at http://tmbeta-genome.cbrc.jp/annotation/.

摘要

我们利用统计方法和机器学习算法开发了数据库TMBETA - GENOME，用于注释基因组序列中的β - 桶状膜蛋白。统计方法基于氨基酸组成、残基对偏好和基序。在机器学习技术中，氨基酸和二肽组成的组合被用作主要属性。此外，已使用基于β - 桶状膜蛋白鉴定以及球状和跨膜螺旋蛋白排除的标准进行注释。已开发出一个网络界面，用于在所有已知基因组中鉴定注释的β - 桶状膜蛋白。用户可以从生命的三个界，即古细菌、细菌和真核生物中选择基因组，并采用五种不同方法。此外，还提供了所有基因组的统计信息以及到不同算法和相关数据库的链接。该数据库可在http://tmbeta - genome.cbrc.jp/annotation/免费获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f2b3/1781149/1876ca3184fd/gkl805f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f2b3/1781149/1876ca3184fd/gkl805f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f2b3/1781149/1876ca3184fd/gkl805f1.jpg

相似文献

1
TMBETA-GENOME: database for annotated beta-barrel membrane proteins in genomic sequences.TMBETA-GENOME：基因组序列中带注释的β-桶状膜蛋白数据库。
Nucleic Acids Res. 2007 Jan;35(Database issue):D314-6. doi: 10.1093/nar/gkl805. Epub 2006 Nov 6.
2
Discrimination of outer membrane proteins using support vector machines.使用支持向量机鉴别外膜蛋白。
Bioinformatics. 2005 Dec 1;21(23):4223-9. doi: 10.1093/bioinformatics/bti697. Epub 2005 Oct 4.
3
TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins.TMBETA-NET：外膜蛋白中跨膜β链的鉴别与预测
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W164-7. doi: 10.1093/nar/gki367.
4
Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.β-桶状外膜蛋白拓扑结构预测方法的评估及一种共识预测方法
BMC Bioinformatics. 2005 Jan 12;6:7. doi: 10.1186/1471-2105-6-7.
5
A consensus algorithm to screen genomes for novel families of transmembrane beta barrel proteins.一种用于筛选基因组中新型跨膜β桶蛋白家族的共识算法。
Proteins. 2007 Oct 1;69(1):8-18. doi: 10.1002/prot.21439.
6
TMB finding pipeline: novel approach for detecting beta-barrel membrane proteins in genomic sequences.肿瘤突变负荷（TMB）发现流程：检测基因组序列中β-桶状膜蛋白的新方法。
J Chem Inf Model. 2007 Nov-Dec;47(6):2456-61. doi: 10.1021/ci700222s. Epub 2007 Oct 24.
7
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes.3D基因组学：一个用于比较已测序基因组之间蛋白质的结构和功能注释的数据库。
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D245-50. doi: 10.1093/nar/gkh064.
8
SwissRegulon: a database of genome-wide annotations of regulatory sites.瑞士调控子数据库：一个全基因组调控位点注释数据库。
Nucleic Acids Res. 2007 Jan;35(Database issue):D127-31. doi: 10.1093/nar/gkl857. Epub 2006 Nov 27.
9
TRAMPLE: the transmembrane protein labelling environment.TRAMPLE：跨膜蛋白标记环境。
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W198-201. doi: 10.1093/nar/gki440.
10
MIPS: analysis and annotation of genome information in 2007.MIPS：2007年基因组信息的分析与注释
Nucleic Acids Res. 2008 Jan;36(Database issue):D196-201. doi: 10.1093/nar/gkm980. Epub 2007 Dec 23.

引用本文的文献

1
OMPdb: A Global Hub of Beta-Barrel Outer Membrane Proteins.OMPdb：β-桶状外膜蛋白的全球信息中心
Front Bioinform. 2021 Apr 9;1:646581. doi: 10.3389/fbinf.2021.646581. eCollection 2021.
2
Prediction of structural features and application to outer membrane protein identification.结构特征预测及其在外膜蛋白识别中的应用。
Sci Rep. 2015 Jun 24;5:11586. doi: 10.1038/srep11586.
3
ProBLM web server: protein and membrane placement and orientation package.ProBLM网络服务器：蛋白质和膜的定位与定向软件包。

本文引用的文献

1
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide.基因组在线数据库（GOLD）v.2：全球基因组计划监测工具
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D332-4. doi: 10.1093/nar/gkj145.
2
Discrimination of outer membrane proteins using support vector machines.使用支持向量机鉴别外膜蛋白。
Bioinformatics. 2005 Dec 1;21(23):4223-9. doi: 10.1093/bioinformatics/bti697. Epub 2005 Oct 4.
3
TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins.TMB-Hunt：用于筛选跨膜β桶蛋白序列集的网络服务器。
Comput Math Methods Med. 2014;2014:838259. doi: 10.1155/2014/838259. Epub 2014 Jul 14.
4
PDBTM: Protein Data Bank of transmembrane proteins after 8 years.PDBTM：经过 8 年的跨膜蛋白数据库。
Nucleic Acids Res. 2013 Jan;41(Database issue):D524-9. doi: 10.1093/nar/gks1169. Epub 2012 Nov 30.
5
OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria.OMPdb：革兰氏阴性菌β桶状外膜蛋白数据库。
Nucleic Acids Res. 2011 Jan;39(Database issue):D324-31. doi: 10.1093/nar/gkq863. Epub 2010 Oct 15.
6
CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources.CoBaltDB：完整的细菌和古菌 ORFeome 亚细胞定位数据库及相关资源。
BMC Microbiol. 2010 Mar 23;10:88. doi: 10.1186/1471-2180-10-88.
7
Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome.绘制大肠杆菌细胞包膜相关蛋白质组和相互作用组的计算与实验方法。
FEMS Microbiol Rev. 2009 Jan;33(1):66-97. doi: 10.1111/j.1574-6976.2008.00141.x. Epub 2008 Nov 27.
8
TMFunction: database for functional residues in membrane proteins.
Nucleic Acids Res. 2009 Jan;37(Database issue):D201-4. doi: 10.1093/nar/gkn672. Epub 2008 Oct 8.
Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W188-92. doi: 10.1093/nar/gki384.
4
Motifs in outer membrane protein sequences: applications for discrimination.外膜蛋白序列中的基序：鉴别应用
Biophys Chem. 2005 Aug 22;117(1):65-71. doi: 10.1016/j.bpc.2005.04.005.
5
Application of residue distribution along the sequence for discriminating outer membrane proteins.沿序列的残基分布在鉴别外膜蛋白中的应用
Comput Biol Chem. 2005 Apr;29(2):135-42. doi: 10.1016/j.compbiolchem.2005.02.006.
6
PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank.PDB_TM：蛋白质数据库中跨膜蛋白的选择与膜定位
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D275-8. doi: 10.1093/nar/gki002.
7
The Universal Protein Resource (UniProt).通用蛋白质资源（UniProt）。
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D154-9. doi: 10.1093/nar/gki070.
8
A simple statistical method for discriminating outer membrane proteins with better accuracy.一种用于更准确地鉴别外膜蛋白的简单统计方法。
Bioinformatics. 2005 Apr 1;21(7):961-8. doi: 10.1093/bioinformatics/bti126. Epub 2004 Nov 5.
9
BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria.BOMP：一种预测革兰氏阴性菌基因组中编码的整合β-桶状外膜蛋白的程序。
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W394-9. doi: 10.1093/nar/gkh351.
10
Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods.使用基于人工神经网络和支持向量机的方法预测β-桶状蛋白的跨膜区域。
Proteins. 2004 Jul 1;56(1):11-8. doi: 10.1002/prot.20092.