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Pfam蛋白质家族数据库。

The Pfam protein families database.

作者信息

Bateman Alex, Coin Lachlan, Durbin Richard, Finn Robert D, Hollich Volker, Griffiths-Jones Sam, Khanna Ajay, Marshall Mhairi, Moxon Simon, Sonnhammer Erik L L, Studholme David J, Yeats Corin, Eddy Sean R

机构信息

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

出版信息

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D138-41. doi: 10.1093/nar/gkh121.

DOI:10.1093/nar/gkh121
PMID:14681378
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC308855/
Abstract

Pfam is a large collection of protein families and domains. Over the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0). Methodology improvements for searching the Pfam collection locally as well as via the web are described. Other recent innovations include modelling of discontinuous domains allowing Pfam domain definitions to be closer to those found in structure databases. Pfam is available on the web in the UK (http://www.sanger.ac.uk/Software/Pfam/), the USA (http://pfam.wustl.edu/), France (http://pfam.jouy.inra.fr/) and Sweden (http://Pfam.cgb.ki.se/).

摘要

Pfam是一个蛋白质家族和结构域的大型集合。在过去两年中，Pfam中的家族数量翻了一番，目前为6190个（10.0版本）。本文描述了在本地以及通过网络搜索Pfam集合的方法改进。最近的其他创新包括对不连续结构域进行建模，使Pfam结构域定义更接近结构数据库中的定义。Pfam在英国（http://www.sanger.ac.uk/Software/Pfam/）、美国（http://pfam.wustl.edu/）、法国（http://pfam.jouy.inra.fr/）和瑞典（http://Pfam.cgb.ki.se/）的网站上均可获取。

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本文引用的文献

1
Enhanced protein domain discovery by using language modeling techniques from speech recognition.
Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4516-20. doi: 10.1073/pnas.0737502100. Epub 2003 Mar 31.
2
E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.
Nucleic Acids Res. 2003 Jan 1;31(1):458-62. doi: 10.1093/nar/gkg065.
3
The CATH database: an extended protein family resource for structural and functional genomics.
Nucleic Acids Res. 2003 Jan 1;31(1):452-5. doi: 10.1093/nar/gkg062.
4
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Nucleic Acids Res. 2003 Jan 1;31(1):365-70. doi: 10.1093/nar/gkg095.
5
The Pfam protein families database.
Nucleic Acids Res. 2002 Jan 1;30(1):276-80. doi: 10.1093/nar/30.1.276.
6
SCOP database in 2002: refinements accommodate structural genomics.
Nucleic Acids Res. 2002 Jan 1;30(1):264-7. doi: 10.1093/nar/30.1.264.
7
Recent improvements to the SMART domain-based sequence annotation resource.
Nucleic Acids Res. 2002 Jan 1;30(1):242-4. doi: 10.1093/nar/30.1.242.
8
PDBsum: summaries and analyses of PDB structures.
Nucleic Acids Res. 2001 Jan 1;29(1):221-2. doi: 10.1093/nar/29.1.221.
9
ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons.
Nucleic Acids Res. 2000 Jan 1;28(1):267-9. doi: 10.1093/nar/28.1.267.
10
The Pfam protein families database.
Nucleic Acids Res. 2000 Jan 1;28(1):263-6. doi: 10.1093/nar/28.1.263.

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