AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses

Nucleic Acids Research
Min HuangJian Zhang

Abstract

Allostery tweaks innumerable biological processes and plays a fundamental role in human disease and drug discovery. Exploration of allostery has thus been regarded as a crucial requirement for research on biological mechanisms and the development of novel therapeutics. Here, based on our previously developed allosteric data and methods, we present an interactive platform called AlloFinder that identifies potential endogenous or exogenous allosteric modulators and their involvement in human allosterome. AlloFinder automatically amalgamates allosteric site identification, allosteric screening and allosteric scoring evaluation of modulator-protein complexes to identify allosteric modulators, followed by allosterome mapping analyses of predicted allosteric sites and modulators in human proteome. This web server exhibits prominent performance in the reemergence of allosteric metabolites and exogenous allosteric modulators in known allosteric proteins. Specifically, AlloFinder enables identification of allosteric metabolites for metabolic enzymes and screening of potential allosteric compounds for disease-related targets. Significantly, the feasibility of AlloFinder to discover allosteric modulators was tested in a real case of signa...Continue Reading

References

Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
May 15, 2003·The Journal of Biological Chemistry·Jing MaXinmin Cao
May 30, 2003·Journal of Medicinal Chemistry·Renxiao WangShaomeng Wang
Jan 26, 2005·Journal of Chemical Information and Modeling·John J Irwin, Brian K Shoichet
Nov 28, 2006·Journal of Chemical Information and Modeling·Jing Chen, Luhua Lai
Dec 13, 2006·Journal of Medicinal Chemistry·Niu HuangJohn J Irwin
Apr 25, 2008·Biochemical and Biophysical Research Communications·Zhiyong RenXiaomin Chen
Jul 22, 2008·Nature Chemical Biology·Nina M Goodey, Stephen J Benkovic
Aug 19, 2008·Trends in Biochemical Sciences·Aron W Fenton
Aug 19, 2008·Journal of Proteome Research·Jeremy K NicholsonPaul Elliott
Jan 1, 2009·Nature Reviews. Drug Discovery·P Jeffrey ConnCraig W Lindsley
Nov 6, 2010·Nucleic Acids Research·Zhimin HuangJian Zhang
Dec 2, 2010·Molecular Systems Biology·Oriol GallegoAnne-Claude Gavin
May 31, 2011·Biochimica Et Biophysica Acta·Joseph L Napoli
Mar 10, 2012·Proceedings of the National Academy of Sciences of the United States of America·Patrick WeinkamAndrej Sali
Apr 5, 2012·Proceedings of the National Academy of Sciences of the United States of America·Balananda-Dhurjati K PutchaElias J Fernandez
Oct 23, 2012·Journal of Molecular Graphics & Modelling·Qi WangJian Zhang
Apr 16, 2013·Cell·Ruth Nussinov, Chung-Jung Tsai
Jun 6, 2013·Nucleic Acids Research·Alexander GoncearencoIgor N Berezovsky
Jul 12, 2013·Bioinformatics·Wenkang HuangJian Zhang
Aug 2, 2013·Nature Reviews. Drug Discovery·Denise WoottenPatrick M Sexton
Dec 3, 2013·Nucleic Acids Research·Zhimin HuangJian Zhang
Dec 7, 2013·Chemical Reviews·Pengxiang HuangFraydoon Rastinejad
Jan 15, 2014·Bioinformatics·Alejandro Panjkovich, Xavier Daura
Apr 5, 2014·PLoS Computational Biology·Gerard J P van WestenJohn P Overington
Apr 18, 2014·Nature·Hesam N MotlaghVincent J Hilser
May 16, 2014·Medicinal Research Reviews·Shaoyong LuJian Zhang
Aug 12, 2014·Drug Discovery Today·Shaoyong LuJian Zhang
Dec 5, 2014·Journal of the American Chemical Society·Ruth NussinovJin Liu
Mar 27, 2015·Bioinformatics·Wenkang HuangJian Zhang
Aug 1, 2015·Journal of Chemical Information and Modeling·Ambrish RoyJeffrey Skolnick
Sep 15, 2015·Nucleic Acids Research·Qiancheng ShenJian Zhang
Oct 20, 2015·Pharmacology & Therapeutics·Edna Zhi Pei ChaiGautam Sethi
Oct 21, 2015·Trends in Biochemical Sciences·Alexandr P Kornev, Susan S Taylor
Oct 27, 2015·BMC Bioinformatics·Joe G Greener, Michael J E Sternberg
Nov 13, 2015·Current Opinion in Structural Biology·Enrico Guarnera, Igor N Berezovsky
Jan 28, 2016·Chemical Reviews·Shaoyong LuJian Zhang
Apr 14, 2016·Chemical Reviews·Jeffrey R WagnerRommie E Amaro
Aug 6, 2016·Molecular Informatics·Ava S-Y ChenJohn B O Mitchell
Aug 28, 2016·Cell·Jean-Pierre Changeux, Arthur Christopoulos
Dec 3, 2016·Nucleic Acids Research·Anna GaultonAndrew R Leach

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Citations

May 14, 2019·Chembiochem : a European Journal of Chemical Biology·Lixin YangLihe Zhang
Dec 10, 2019·The Journal of Experimental Medicine·Yirong WangYifeng Zhou
Feb 6, 2020·International Journal of Molecular Sciences·Olivier Sheik AmamuddyOzlem Tastan Bishop
Apr 18, 2019·Scientific Reports·Amanda E WakefieldGyörgy M Keserű
Jan 24, 2020·Frontiers in Chemistry·Zarko GagicKatarina Nikolic
Feb 9, 2019·Journal of Enzyme Inhibition and Medicinal Chemistry·Xinyuan XuShaoyong Lu
Oct 31, 2019·Nucleic Acids Research·Xinyi LiuJian Zhang
May 10, 2019·Nucleic Acids Research·Kun SongJian Zhang
Nov 28, 2018·Physical Chemistry Chemical Physics : PCCP·Longrong WangXuemei Pu
Dec 22, 2020·Frontiers in Molecular Biosciences·Irène PitardThérèse E Malliavin
Dec 8, 2019·Structure·Zhuyezi SunSandor Vajda
Apr 13, 2021·The Journal of Physical Chemistry. B·Wei-Ven TeeIgor N Berezovsky
Mar 1, 2019·Journal of Medicinal Chemistry·Shaoyong LuJian Zhang
Dec 23, 2021·Expert Opinion on Drug Discovery·Ashfaq Ur RehmanJian Zhang

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