AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization

Journal of Chemical Information and Modeling
Yan LiRen-Xiao Wang

Abstract

In structure-based drug design, automated de novo design methods are helpful tools for lead discovery as well as lead optimization. In a previous study ( J. Chem. Inf. 2011 , 51 , 1474 - 1491 ) we reported a new de novo design method, namely, Automatic Tailoring and Transplanting (AutoT&T). It overcomes some intrinsic problems in conventional fragment-based buildup methods. In this study, we describe an upgraded version, namely, AutoT&T2. Structural operations conducted by AutoT&T2 have been largely optimized by introducing several new algorithms. As a result, its overall speed in multiround optimization jobs has been improved by a few thousand fold. With this improvement, it is now practical to conduct structural crossover among multiple lead molecules using AutoT&T2. Three different test cases are described in this study that demonstrate the new features and versatile applications of AutoT&T2. The AutoT&T2 software suite is available to the public. Besides, a Web portal for running AutoT&T2 online is provided at http://www.sioc-ccbg.ac.cn/software/att2 for testing.

References

Feb 1, 1992·Journal of Computer-aided Molecular Design·H J Böhm
Jun 1, 1995·Journal of Computer-aided Molecular Design·D C Roe, I D Kuntz
Apr 1, 1995·Journal of Computer-aided Molecular Design·D R WestheadB Waszkowycz
Feb 1, 1995·Journal of Computer-aided Molecular Design·D E ClarkD R Westhead
Jan 1, 1994·Journal of Chemical Information and Computer Sciences·V J GilletA P Johnson
Feb 1, 1993·Journal of Computer-aided Molecular Design·S H Rotstein, M A Murcko
Jul 19, 1996·Journal of Medicinal Chemistry·G W Bemis, M A Murcko
Nov 7, 1998·Journal of Medicinal Chemistry·G S WestonB K Shoichet
Jul 12, 2002·Journal of Medicinal Chemistry·Rachel A Powers, Brian K Shoichet
Jan 24, 2003·Nature·Ramanathan NateshK Ravi Acharya
Jun 13, 2003·Journal of Medicinal Chemistry·H Maarten VinkersPaul A J Janssen
Apr 2, 2005·Journal of Medicinal Chemistry·Dominique DouguetSylvie Pochet
Apr 20, 2005·Bioorganic & Medicinal Chemistry Letters·Yasushi MiyazakiRobert T Nolte
Aug 2, 2005·Nature Reviews. Drug Discovery·Gisbert Schneider, Uli Fechner
Oct 9, 2007·Journal of Medicinal Chemistry·Qian LiuJulian Smith
Nov 8, 2007·Journal of Chemical Information and Modeling·Tiejun ChengLuhua Lai
Feb 11, 2009·Journal of Medicinal Chemistry·Michele H Potashman, Mark E Duggan
Jun 17, 2009·Journal of Chemical Information and Modeling·Peter S KutchukianEugene I Shakhnovich
Nov 26, 2009·Current Topics in Medicinal Chemistry·Kathryn LovingWoody Sherman
May 11, 2010·Bioorganic & Medicinal Chemistry Letters·Donatella TondiMaria Paola Costi
Apr 26, 2011·Journal of Chemical Information and Modeling·Yaxia YuanLuhua Lai
Apr 28, 2011·Journal of Chemical Information and Modeling·Yan LiRenxiao Wang
Feb 24, 2012·PLoS Computational Biology·Markus HartenfellerGisbert Schneider
May 9, 2012·Journal of Chemical Information and Modeling·Fung-Yi ChanKwok-Yin Wong
Aug 1, 2010·Expert Opinion on Drug Discovery·Peter S Kutchukian, Eugene I Shakhnovich
Apr 27, 2013·Journal of Chemical Information and Modeling·Andrea R BeccariGabriele Costantino
Nov 10, 2013·Nucleic Acids Research·Vivian LawDavid S Wishart
Feb 5, 2014·Journal of Chemical Information and Modeling·Diane Joseph-McCarthyDemetri Moustakas
Oct 11, 2014·Bioinformatics·Zhihai LiuRenxiao Wang
Oct 27, 2014·Nature Chemical Biology·Nir LondonJack Taunton
Dec 1, 2014·Molecular Informatics·Kazuaki MishimaKimito Funatsu

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Citations

Jan 10, 2017·Expert Opinion on Drug Discovery·Rajan ChaudhariShuxing Zhang
Apr 11, 2018·The AAPS Journal·Yuemin Bian, Xiang-Qun Sean Xie
Jul 28, 2018·Molecular Informatics·Laurent HofferXavier Morelli
May 27, 2020·Expert Opinion on Drug Discovery·Rajan ChaudhariShuxing Zhang
Oct 8, 2019·European Journal of Medicinal Chemistry·Yunyuan HuangJian Wan
Jan 13, 2021·Journal of Cheminformatics·Jacob O Spiegel, Jacob D Durrant
Dec 5, 2020·Journal of Chemical Information and Modeling·Jinwen ShanChangge Ji
Oct 28, 2019·Journal of Chemical Information and Modeling·Yan LiRenxiao Wang

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