Suppr超能文献

Pfam蛋白质家族数据库。

The Pfam protein families database.

作者信息

Bateman Alex, Birney Ewan, Cerruti Lorenzo, Durbin Richard, Etwiller Laurence, Eddy Sean R, Griffiths-Jones Sam, Howe Kevin L, Marshall Mhairi, Sonnhammer Erik L L

机构信息

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

出版信息

Nucleic Acids Res. 2002 Jan 1;30(1):276-80. doi: 10.1093/nar/30.1.276.

DOI:10.1093/nar/30.1.276
PMID:11752314
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC99071/
Abstract

Pfam is a large collection of protein multiple sequence alignments and profile hidden Markov models. Pfam is available on the World Wide Web in the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the US at http://pfam.wustl.edu/. The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins in SWISS-PROT 39 and TrEMBL 14. Structural data, where available, have been utilised to ensure that Pfam families correspond with structural domains, and to improve domain-based annotation. Predictions of non-domain regions are now also included. In addition to secondary structure, Pfam multiple sequence alignments now contain active site residue mark-up. New search tools, including taxonomy search and domain query, greatly add to the functionality and usability of the Pfam resource.

摘要

Pfam是蛋白质多序列比对和轮廓隐马尔可夫模型的一个大型集合。Pfam在英国可通过万维网访问，网址为http://www.sanger.ac.uk/Software/Pfam/；在瑞典为http://www.cgb.ki.se/Pfam/；在法国为http://pfam.jouy.inra.fr/；在美国为http://pfam.wustl.edu/。Pfam的最新版本（6.6）包含3071个家族，与SWISS-PROT 39和TrEMBL 14中69%的蛋白质相匹配。已利用现有的结构数据来确保Pfam家族与结构域相对应，并改进基于结构域的注释。现在还包括对非结构域区域的预测。除二级结构外，Pfam多序列比对现在还包含活性位点残基标记。新的搜索工具，包括分类学搜索和结构域查询，极大地增强了Pfam资源的功能和可用性。

相似文献

1
The Pfam protein families database.
Nucleic Acids Res. 2002 Jan 1;30(1):276-80. doi: 10.1093/nar/30.1.276.
2
Pfam: clans, web tools and services.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D247-51. doi: 10.1093/nar/gkj149.
3
Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.
Nucleic Acids Res. 1999 Jan 1;27(1):260-2. doi: 10.1093/nar/27.1.260.
4
The Pfam protein families database.
Nucleic Acids Res. 2000 Jan 1;28(1):263-6. doi: 10.1093/nar/28.1.263.
5
The Pfam protein families database.
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D138-41. doi: 10.1093/nar/gkh121.
6
The Pfam protein families database.
Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8. doi: 10.1093/nar/gkm960. Epub 2007 Nov 26.
7
Pfam: multiple sequence alignments and HMM-profiles of protein domains.
Nucleic Acids Res. 1998 Jan 1;26(1):320-2. doi: 10.1093/nar/26.1.320.
8
The Pfam protein families database.
Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22. doi: 10.1093/nar/gkp985. Epub 2009 Nov 17.
9
SUPFAM--a database of potential protein superfamily relationships derived by comparing sequence-based and structure-based families: implications for structural genomics and function annotation in genomes.
Nucleic Acids Res. 2002 Jan 1;30(1):289-93. doi: 10.1093/nar/30.1.289.
10
Identifying protein domains with the Pfam database.
Curr Protoc Bioinformatics. 2008 Sep;Chapter 2:2.5.1-2.5.17. doi: 10.1002/0471250953.bi0205s23.

引用本文的文献

1
Machine Learning Approaches for the Identification of Genetic Interactions.
Methods Mol Biol. 2025;2952:259-272. doi: 10.1007/978-1-0716-4690-8_15.
2
Molecular complexity of the differential growth of freshwater diatoms along pH gradients.
ISME Commun. 2025 May 6;5(1):ycaf078. doi: 10.1093/ismeco/ycaf078. eCollection 2025 Jan.
3
A Novel in an Bat from Nairobi, Kenya.
Viruses. 2025 Apr 12;17(4):557. doi: 10.3390/v17040557.
4
Comprehensive analysis of the NAC transcription factor gene family in Sophora tonkinensis Gagnep.
BMC Plant Biol. 2025 Apr 25;25(1):530. doi: 10.1186/s12870-025-06564-0.
5
Ultrasound-activated nano-oxygen sensitizer for sonodynamic-radiotherapy of esophageal cancer.
Nanoscale Adv. 2025 Feb 20;7(8):2209-2221. doi: 10.1039/d5na00042d. eCollection 2025 Apr 8.
6
LEA_4 motifs function alone and in conjunction with synergistic cosolutes to protect a labile enzyme during desiccation.
Protein Sci. 2025 Feb;34(2):e70028. doi: 10.1002/pro.70028.
7
The molecular toll pathway repertoire in anopheline mosquitoes.
Dev Comp Immunol. 2025 Jan;162:105287. doi: 10.1016/j.dci.2024.105287. Epub 2024 Nov 8.
8
Protein A-like Peptide Design Based on Diffusion and ESM2 Models.
Molecules. 2024 Oct 21;29(20):4965. doi: 10.3390/molecules29204965.
9
The Molecular Toll Pathway Repertoire in Anopheline Mosquitoes.
bioRxiv. 2024 Sep 18:2024.09.12.612760. doi: 10.1101/2024.09.12.612760.
10
Full-length transcriptome sequencing of pepper fruit during development and construction of a transcript variation database.
Hortic Res. 2024 Jul 24;11(9):uhae198. doi: 10.1093/hr/uhae198. eCollection 2024 Sep.

本文引用的文献

1
NIFAS: visual analysis of domain evolution in proteins.
Bioinformatics. 2001 Apr;17(4):343-8. doi: 10.1093/bioinformatics/17.4.343.
2
Initial sequencing and analysis of the human genome.
Nature. 2001 Feb 15;409(6822):860-921. doi: 10.1038/35057062.
3
InterPro--an integrated documentation resource for protein families, domains and functional sites.
Bioinformatics. 2000 Dec;16(12):1145-50. doi: 10.1093/bioinformatics/16.12.1145.
4
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.
J Mol Biol. 2001 Jan 19;305(3):567-80. doi: 10.1006/jmbi.2000.4315.
5
PDBsum: summaries and analyses of PDB structures.
Nucleic Acids Res. 2001 Jan 1;29(1):221-2. doi: 10.1093/nar/29.1.221.
6
TIGRFAMs: a protein family resource for the functional identification of proteins.
Nucleic Acids Res. 2001 Jan 1;29(1):41-3. doi: 10.1093/nar/29.1.41.
7
The genome sequence of Drosophila melanogaster.
Science. 2000 Mar 24;287(5461):2185-95. doi: 10.1126/science.287.5461.2185.
8
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.
9
Machine learning approaches for the prediction of signal peptides and other protein sorting signals.
Protein Eng. 1999 Jan;12(1):3-9. doi: 10.1093/protein/12.1.3.
10
SMART: identification and annotation of domains from signalling and extracellular protein sequences.
Nucleic Acids Res. 1999 Jan 1;27(1):229-32. doi: 10.1093/nar/27.1.229.

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

文档翻译

学术文献翻译模型，支持多种主流文档格式。

立即体验