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LICEDB:用于工业应用和人工智能酶设计的轻工业核心酶数据库。

LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design.

作者信息

Gong Lei, Liu Fufeng, Zhang Chuanxi, Ming Yongfan, Mou Yulan, Yuan ZhaoTing, Jiang Haiming, Gao Bei, Lu Fuping, Zhang Lujia

机构信息

School of Chemistry and Molecular Engineering, East China Normal University, No.500 Dongchuan Road, Minhang District, Shanghai, China, Shanghai 200062, China.

School of Biotechnology, Tianjin University of Science and Technology, No.9, 13th Street, Economic and Technological Development Zone, Binhai New Area, Tianjin 300457, China.

出版信息

Database (Oxford). 2025 Feb 19;2025. doi: 10.1093/database/baaf001.

DOI:10.1093/database/baaf001
PMID:39980225
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11842304/
Abstract

Enzymes, serving as eco-friendly catalysts, are progressively supplanting traditional chemical catalysts in light industry sectors such as feed, papermaking, textiles, detergents, leather, and sugar production. Despite this advancement, the variability in the performance of natural enzymes and the fragmentation and diversity of existing data formats pose significant challenges to researchers. Furthermore, AI-driven enzyme design is limited by the quality and quantity of available data. To address these issues, we introduce the light industrial core enzyme database (LICEDB), the first database dedicated exclusively to managing and standardizing enzymes for light industry applications. LICEDB, with its integrated modules for data retrieval, similarity analysis, and structural analysis, will enhance the efficient industrial application of enzymes and strengthen AI-driven predictive research, thereby advancing data sharing and utilization in the field of enzyme innovation. Database URL: http://lujialab.org.cn/on-line-databases/.

摘要

酶作为环境友好型催化剂,正在逐步取代饲料、造纸、纺织、洗涤剂、皮革和制糖等轻工业领域中的传统化学催化剂。尽管取得了这一进展,但天然酶性能的变异性以及现有数据格式的碎片化和多样性给研究人员带来了重大挑战。此外,人工智能驱动的酶设计受到可用数据质量和数量的限制。为了解决这些问题,我们引入了轻工业核心酶数据库(LICEDB),这是首个专门用于管理和规范轻工业应用酶的数据库。LICEDB具有数据检索、相似性分析和结构分析的集成模块,将提高酶的高效工业应用,并加强人工智能驱动的预测研究从而推动酶创新领域的数据共享和利用。数据库网址:http://lujialab.org.cn/on-line-databases/

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f8db/11842304/12f53c497bbf/baaf001f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f8db/11842304/c88fa5819189/baaf001fa1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f8db/11842304/28b11a67d8f6/baaf001f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f8db/11842304/80e50a56cdb5/baaf001f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f8db/11842304/6af204dc81a1/baaf001f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f8db/11842304/12f53c497bbf/baaf001f4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f8db/11842304/c88fa5819189/baaf001fa1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f8db/11842304/28b11a67d8f6/baaf001f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f8db/11842304/80e50a56cdb5/baaf001f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f8db/11842304/6af204dc81a1/baaf001f3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f8db/11842304/12f53c497bbf/baaf001f4.jpg

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本文引用的文献

1
Descriptor-augmented machine learning for enzyme-chemical interaction predictions.用于酶-化学相互作用预测的描述符增强机器学习
Synth Syst Biotechnol. 2024 Feb 28;9(2):259-268. doi: 10.1016/j.synbio.2024.02.006. eCollection 2024 Jun.
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Artificial Intelligence-Powered Construction of a Microbial Optimal Growth Temperature Database and Its Impact on Enzyme Optimal Temperature Prediction.人工智能驱动构建微生物最佳生长温度数据库及其对酶最佳温度预测的影响。
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UniKP: a unified framework for the prediction of enzyme kinetic parameters.
UniKP:一种用于预测酶动力学参数的统一框架。
Nat Commun. 2023 Dec 11;14(1):8211. doi: 10.1038/s41467-023-44113-1.
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Turnover number predictions for kinetically uncharacterized enzymes using machine and deep learning.使用机器学习和深度学习预测动力学特征未知的酶的周转率。
Nat Commun. 2023 Jul 12;14(1):4139. doi: 10.1038/s41467-023-39840-4.
5
Enzyme Commission Number Prediction and Benchmarking with Hierarchical Dual-core Multitask Learning Framework.基于分层双核多任务学习框架的酶委员会编号预测与基准测试
Research (Wash D C). 2023 May 31;6:0153. doi: 10.34133/research.0153. eCollection 2023.
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A general model to predict small molecule substrates of enzymes based on machine and deep learning.基于机器学习和深度学习的酶小分子底物通用预测模型。
Nat Commun. 2023 May 15;14(1):2787. doi: 10.1038/s41467-023-38347-2.
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dbMisLoc: A Manually Curated Database of Conditional Protein Mis-localization Events.dbMisLoc:一个人工 curated 的条件性蛋白质定位错误事件数据库。
Interdiscip Sci. 2023 Sep;15(3):433-438. doi: 10.1007/s12539-023-00564-0. Epub 2023 Mar 31.
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Enzyme function prediction using contrastive learning.使用对比学习进行酶功能预测。
Science. 2023 Mar 31;379(6639):1358-1363. doi: 10.1126/science.adf2465. Epub 2023 Mar 30.
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Designer installation of a substrate recruitment domain to tailor enzyme specificity.设计底物募集结构域的安装,以定制酶的特异性。
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