Protein domain analysis in the era of complete genomes

FEBS Letters
Richard R CopleyPeer Bork

Abstract

Domains present one of the most useful levels at which to understand protein function, and domain family-based analysis has had a profound impact on the study of individual proteins. Protein domain discovery has been progressing steadily over the past 30 years. What are the realistically achievable goals of sequence-based domain analysis, and how far off are they for the sequences encoded in eukaryotic genomes? Here we address some of the issues involved in better coverage of sequence-based domain annotation, and the integration of these results within the wider context of genomes, structures and function.

References

Jan 1, 1985·Methods in Enzymology·J Janin, C Chothia
Mar 1, 1994·Protein Science : a Publication of the Protein Society·E L Sonnhammer, D Kahn
Mar 29, 1996·Journal of Molecular Biology·O LichtargeF E Cohen
Nov 1, 1996·Protein Science : a Publication of the Protein Society·C P Ponting
Jan 27, 1999·Bioinformatics·X Guan, L Du
Dec 11, 1999·Nucleic Acids Research·J SchultzP Bork
Dec 11, 1999·Nucleic Acids Research·L Lo ConteC Chothia
Dec 11, 1999·Nucleic Acids Research·A BatemanE L Sonnhammer
Jun 1, 2000·Advances in Protein Chemistry·C P PontingP Bork
Jun 14, 2000·Journal of Molecular Biology·Y I WolfE V Koonin
Jun 28, 2000·Bioinformatics·A J Enright, C A Ouzounis
Oct 7, 2000·Journal of Molecular Biology·S S Hannenhalli, R B Russell
Oct 13, 2000·Science·H OgataJ M Claverie
Feb 13, 2001·Nucleic Acids Research·N V Grishin
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Apr 3, 2001·Proceedings of the National Academy of Sciences of the United States of America·T ItoY Sakaki
Apr 11, 2001·Bioinformatics·A Heger, L Holm
Apr 13, 2001·Bioinformatics·R Spang, M Vingron
May 25, 2001·Nature Structural Biology·D VitkupC Sander
Jun 28, 2001·Nature Structural Biology·K E Prehoda, W A Lim
Jun 28, 2001·Nature Structural Biology·M HopfE Hohenester
Sep 12, 2001·Journal of Structural Biology·M A AndradeC P Ponting
Sep 12, 2001·Journal of Structural Biology·N V Grishin
Nov 13, 2001·Developmental Cell·J TothC J Harrison

❮ Previous
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Citations

Jul 14, 2006·Bioinformatics·Kui LinDa-Yong Zhang
May 24, 2011·Genome Biology and Evolution·Mary M Rorick, Günter P Wagner
Sep 23, 2003·Nucleic Acids Research·Noam KaplanMichal Linial
Jul 18, 2006·Nucleic Acids Research·Maria NovatchkovaAlexander Schleiffer
Nov 4, 2008·Nucleic Acids Research·Ivica LetunicPeer Bork
Nov 8, 2002·Genome Research·Henrik KaessmannWen-Hsiung Li
Oct 14, 2008·Journal of Bacteriology·Amoolya H SinghPeer Bork
Jun 6, 2012·International Journal of Peptides·Mythily Srinivasan, A Keith Dunker
Oct 27, 2004·BMC Bioinformatics·Jer-Ming Chia, Prasanna R Kolatkar
Jun 17, 2008·BMC Bioinformatics·Chilamakuri C S ReddyRamanathan Sowdhamini
Mar 20, 2008·BMC Bioinformatics·Paul D YooAlbert Y Zomaya
Oct 16, 2008·BMC Evolutionary Biology·January WeinerErich Bornberg-Bauer
Mar 15, 2006·BMC Genomics·Danielle KemmerWyeth W Wasserman
Mar 11, 2009·Frontiers in Bioscience (Landmark Edition)·Francis C Peterson, Brian F Volkman
Jul 5, 2007·Journal of the Air & Waste Management Association·Eric M FujitaDouglas R Lawson
Dec 6, 2008·Nucleic Acids Research·Rajkumar BondugulaAnders Wallqvist
Apr 28, 2009·Current Opinion in Structural Biology·Ruben E ValasPhilip E Bourne
Sep 4, 2015·Protein Science : a Publication of the Protein Society·Haiming HuangSachdev S Sidhu
Jan 25, 2008·Proteins·Xing-Ming ZhaoKazuyuki Aihara
Apr 20, 2016·Protoplasma·Markus LanghansTobias Meckel
Jun 17, 2008·IEEE Transactions on Nanobioscience·P D YooA Y Zomaya
Jun 25, 2005·Protein Engineering, Design & Selection : PEDS·Dinesh C SoaresPaul N Barlow
Jun 8, 2017·International Journal of Molecular Sciences·Sofie Van HolleEls J M Van Damme
Aug 12, 2004·Chemical Reviews·Andrew R Pickford, Iain D Campbell
Nov 26, 2009·Science Signaling·Jing JinTony Pawson

❮ Previous
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