将各种生物活性数据集成到化学检查器化合物宇宙中
Arnau Comajuncosa-Creus1, Martino Bertoni1, Miquel Duran-Frigola1
1Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.
Nature protocols
|May 21, 2025
概括
这项研究介绍了一种计算协议,用于使用深度神经网络和化学检查器数据库为小分子生成动态生物活性签名. 这种方法有效地将化合物注释扩展到更大的化学景观中.
科学领域:
- 计算化学是一种计算化学.
- 生物信息学是一种生物信息学.
- 机器学习是机器学习.
背景情况:
- 化学签名是小分子的数值描述符,对于比较和搜索至关重要.
- 现有的生物活性描述符仅限于经过充分记录的化合物,阻碍了全面的分析.
- 深度神经网络可以从可用的实验数据中推断出缺失的生物活性签名.
研究的目的:
- 介绍一种用于生成和修改生物活性空间和签名的计算协议.
- 通过化学检查器 (CC) 知识库,利用各种生物活性数据.
- 为了使更大的化学景观的注释能够超越记录良好的分子.
主要方法:
- 实施深度神经网络以推断生物活性特征.
- 在化学检查器框架内使用预定义的数据处理管道.
- 通过示例进行演示:结合新化合物,改变数据预处理,创造新的生物活性空间.
主要成果:
- 该协议可以修改或生成新的生物活性空间和签名.
- 四个具体的例子说明了议定书的灵活性和应用.
- 使用GPU计算,在不到9个小时的时间内从零开始创建了新的生物活性空间.
结论:
- 该协议提供了一个指导方针,用于将用户提供的数据与CC方法集成.
- 它将生物活性注释扩展到更广泛的小分子.
- 新的,动态的生物活性特征被生成用于增强化学分析.
更多相关视频
09:04Identifying Per- and Polyfluorinated Chemical Species with a Combined Targeted and Non-Targeted-Screening High-Resolution Mass Spectrometry Workflow
Published on: April 18, 2019
12.3K
07:51High-throughput Identification of Synergistic Drug Combinations by the Overlap2 Method
Published on: May 21, 2018
11.6K
相关概念视频
Structure-Activity Relationships and Drug Design
474
Drug design is a dynamic field that involves discovering and developing new medications based on specific biological targets. This process heavily relies on structure-activity relationships (SAR) and quantitative structure-activity relationships (QSAR) to guide the design and optimization of efficient drugs.
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence...
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence...
474
Drug Discovery: Overview
7.3K
Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...
7.3K
Effects of Chemicals: Overview
1.2K
Drugs, encompassing various chemical compounds from natural sources, lab synthesis, or genetic engineering, elicit different biological responses in living organisms. Some of these responses are desirable or therapeutic, while others are undesirable. The primary goal of administering a drug is to achieve a therapeutic effect, that is, to address a specific disease or health condition. Any concurrent effects outside of this therapeutic outcome are considered undesirable. These undesirable...
1.2K
