Journal
JOURNAL OF CHEMICAL INFORMATION AND MODELING
Volume 56, Issue 2, Pages 435-453Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jcim.5b00691
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Funding
- Ministry of Science and Technology of China [2012AA020308]
- National Natural Science Foundation of China [21102168, 81430083, 81172984, 21072213]
- Science and Technology Development Fund of Macao SAR [055/2013/A2]
- Amgen Biopharmaceutical Research & Development (Shanghai) Co., Ltd.
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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. Model. 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.
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