Predicting protein interface residues using easily accessible on-line resources

Briefings in Bioinformatics
Surabhi Maheshwari, Michal Brylinski

Abstract

It has been more than a decade since the completion of the Human Genome Project that provided us with a complete list of human proteins. The next obvious task is to figure out how various parts interact with each other. On that account, we review 10 methods for protein interface prediction, which are freely available as web servers. In addition, we comparatively evaluate their performance on a common data set comprising different quality target structures. We find that using experimental structures and high-quality homology models, structure-based methods outperform those using only protein sequences, with global template-based approaches providing the best performance. For moderate-quality models, sequence-based methods often perform better than those structure-based techniques that rely on fine atomic details. We note that post-processing protocols implemented in several methods quantitatively improve the results only for experimental structures, suggesting that these procedures should be tuned up for computer-generated models. Finally, we anticipate that advanced meta-prediction protocols are likely to enhance interface residue prediction. Notwithstanding further improvements, easily accessible web servers already provide th...Continue Reading

References

Jan 9, 1996·Proceedings of the National Academy of Sciences of the United States of America·S Jones, J M Thornton
Mar 29, 1996·Journal of Molecular Biology·O LichtargeF E Cohen
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Sep 23, 1997·Journal of Molecular Biology·S Jones, J M Thornton
Sep 23, 1997·Journal of Molecular Biology·S Jones, J M Thornton
Nov 21, 1997·Journal of Molecular Biology·R A Abagyan, S Batalov
Oct 27, 1998·Trends in Biochemical Sciences·K Henrick, J M Thornton
Dec 10, 1998·Nucleic Acids Research·T J HubbardC Chothia
Apr 14, 1999·Proceedings of the National Academy of Sciences of the United States of America·M PellegriniT O Yeates
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Mar 4, 2000·Proceedings of the National Academy of Sciences of the United States of America·M E SowaO Lichtarge
May 31, 2001·Journal of Molecular Graphics & Modelling·A K DunkerZ Obradovic
Sep 17, 2002·Briefings in Bioinformatics·Nicola J MulderUNKNOWN InterPro Consortium
Dec 31, 2002·Current Opinion in Structural Biology·Frank Sobott, Carol V Robinson
Mar 22, 2003·Current Opinion in Cell Biology·Martijn A HuynenPeer Bork
Jun 5, 2003·FEBS Letters·Yanay Ofran, Burkhard Rost
Jun 5, 2003·Proteins·Rong ChenZhiping Weng
Dec 24, 2003·Protein Science : a Publication of the Protein Society·Daniel R CaffreyEnoch S Huang
Mar 24, 2004·Current Opinion in Chemical Biology·Tanja Kortemme, David Baker
Mar 30, 2004·Protein Engineering, Design & Selection : PEDS·Asako Koike, Toshihisa Takagi
Mar 31, 2004·Journal of Molecular Biology·Hani NeuvirthGideon Schreiber
Oct 21, 2004·Proteins·Juan Fernandez-RecioRuben Abagyan
Apr 29, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Michael WagnerJarosław Meller
May 21, 2005·Proteins·Andrew J Bordner, Ruben Abagyan
Oct 6, 2005·Physical Biology·András SzilágyiJeffrey Skolnick
Feb 2, 2006·Proteins·Sjoerd J de VriesAlexandre M J J Bonvin
Apr 8, 2006·International Journal of Biological Macromolecules·Jing-Jing LiPen Chen
Aug 9, 2006·Nucleic Acids Research·Shide LiangYaoqi Zhou
Aug 29, 2006·Journal of Molecular Biology·Amrita MohanVladimir N Uversky
Dec 13, 2006·Proteins·Gajinder Pal SinghDebasis Dash
Dec 16, 2006·Protein and Peptide Letters·Bing WangDe-Shuang Huang

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Citations

Jul 17, 2015·Protein Science : a Publication of the Protein Society·Howook HwangBarry Honig
Aug 4, 2015·Methods : a Companion to Methods in Enzymology·Surabhi Maheshwari, Michal Brylinski
Jan 3, 2016·The Journal of Chemical Physics·Sam Tonddast-Navaei, Jeffrey Skolnick
Oct 14, 2017·Bioinformatics·Francesca Nadalin, Alessandra Carbone
Feb 8, 2018·BMC Bioinformatics·Sebastian Daberdaku, Carlo Ferrari
Jan 23, 2018·Nature Methods·Michael J MeyerHaiyuan Yu
Mar 24, 2017·Briefings in Bioinformatics·Jian Zhang, Lukasz Kurgan
Dec 3, 2016·Proceedings of the National Academy of Sciences of the United States of America·Fang BaiJosé N Onuchic
Jul 1, 2015·The Journal of Biological Chemistry·Daniel E CooperRosalind A Coleman
Dec 13, 2017·Proceedings of the National Academy of Sciences of the United States of America·Howook HwangBarry Honig
Jul 25, 2019·Frontiers in Microbiology·Kleber Santiago Freitas E SilvaMaristela Pereira
Jun 16, 2018·Nucleic Acids Research·Sébastien ReilleGuillaume Launay
Oct 30, 2020·Nucleic Acids Research·Bi ZhaoLukasz Kurgan
Jun 18, 2019·Journal of Molecular Biology·Eric T C Wong, Jörg Gsponer
Aug 21, 2021·Briefings in Bioinformatics·Jian ZhangLukasz Kurgan

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