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READRetro网络:一个用于预测植物天然产物生物合成的用户友好型平台。

READRetro web: A user-friendly platform for predicting plant natural product biosynthesis.

作者信息

Kwak Yejin, Kim Taein, Kim Sang-Gyu, Park Jeongbin

机构信息

Medical Research Institute, Pusan National University, Yangsan, Republic of Korea.

Department of Biological Sciences, KAIST, Daejeon, Korea.

出版信息

Mol Cells. 2025 Jun 2;48(8):100235. doi: 10.1016/j.mocell.2025.100235.

Abstract

Natural products (NPs), a fundamental class of bioactive molecules with broad applicability, are valuable sources in pharmaceutical research and drug discovery. Despite their significance, the large-scale production of NPs is often limited by their availability and scalability, requiring alternative approaches such as metabolic engineering or biosynthesis. To identify ideal pathways for the mass production of NPs, deep learning-based retrosynthesis models have been recently developed. Such models accelerate NP discovery; however, these tools are often not easy to use for researchers with a limited computational background, because they require complex environment configurations, command-line interfaces, and substantial computational resources. Here, we introduce READRetro web, a user-friendly web platform that integrates the READRetro machine learning (ML) model for retrosynthesis prediction. Based on modern web technologies, our web platform provides a fast and responsive user experience. READRetro Web bridges the gap between advanced ML-driven retrosynthesis and practical research workflows, making retrosynthesis prediction accessible to a broader range of researchers. Our platform demonstrates high predictive accuracy and computational efficiency, offering well-organized results to facilitate NP retrosynthetic pathway design. READRetro Web is freely accessible via https://readretro.net.

摘要

天然产物(NPs)是一类具有广泛适用性的生物活性分子,是药物研究和药物发现的宝贵来源。尽管它们很重要,但NPs的大规模生产往往受到其可得性和可扩展性的限制,需要代谢工程或生物合成等替代方法。为了确定NPs大规模生产的理想途径,最近开发了基于深度学习的逆合成模型。这类模型加速了NPs的发现;然而,对于计算背景有限的研究人员来说,这些工具通常不容易使用,因为它们需要复杂的环境配置、命令行界面和大量的计算资源。在这里,我们介绍READRetro web,这是一个用户友好的网络平台,集成了用于逆合成预测的READRetro机器学习(ML)模型。基于现代网络技术,我们的网络平台提供了快速响应的用户体验。READRetro Web弥合了先进的机器学习驱动的逆合成与实际研究工作流程之间的差距,使更广泛的研究人员能够进行逆合成预测。我们的平台展示了高预测准确性和计算效率,提供了组织良好的结果以促进NPs逆合成途径设计。可通过https://readretro.net免费访问READRetro Web。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/909d/12219344/21e928006bdf/gr1.jpg

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