预先训练的模型真的可以学习更好的分子表示,以获得人工智能辅助的药物发现吗?
Ziqiao Zhang1, Yatao Bian2, Ailin Xie1
1Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200438, China.
Journal of chemical information and modeling
|December 25, 2023
概括
我们开发了代表性-财产关系分析 (RePRA) 来评估人工智能模型生成的药物发现分子表示. RePRA揭示,虽然一些模型改进了传统方法,但其他模型可能会产生低于最佳的表示,指导未来的AI开发.
科学领域:
- 计算化学的计算化学
- 人工智能的人工智能
- 药物发现 药物发现 药物发现
背景情况:
- 自主监督的预训练模型越来越多地用于用于分子表示的AI辅助药物发现.
- 从这些模型中学习到的表示的质量仍然未被充分探索.
- 传统的定量结构-活动关系 (QSAR) 分析利用活动悬崖 (ACs) 和脚手架跳跃 (SH).
研究的目的:
- 提出和分析一种新的方法,即表示与属性关系分析 (RePRA),用于评估分子表示质量.
- 将AC和SH的概念从结构-活动到表示-属性上下文进行概括.
- 为评估预训练模型在产生有意义的分子特征方面的有效性提供一个框架.
主要方法:
- 将活动悬崖 (ACs) 和脚手架跳跃 (SH) 的概念推广到表示-属性领域.
- 开发了RePRA来分析分子表示和属性之间的关系.
- 设计了两个分数来量化概括AC和SH用于表示质量评估.
- 在10个目标任务中分析了7个预训练模型的分子表示.
主要成果:
- 最先进的预训练模型在某些方面显示出比标准的扩展连接指纹 (ECFP) 更好的改进.
- 代表空间和分子子结构之间的明确相关性并不总是清楚的.
- 一些预训练的模型产生了比ECFPs更低效的表示.
- RePRA成功评估了分子表示的质量.
结论:
- RePRA为研究人员提供了一种强大的方法,用于评估自主监督预训模型的分子表示.
- 研究结果强调需要更好的预训练技术来规范AC和SH,以改善药物发现.
- 该研究指导开发更可靠的AI模型,用于药物发现中的特征提取.
相关概念视频
Drug Discovery: Overview
7.9K
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...
7.9K
Ligand Binding Sites
12.9K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.9K
Protein-protein Interfaces
12.5K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.5K
Structure-Activity Relationships and Drug Design
727
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...
727
Protein Organization
6.5K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
The primary structure of a protein is its amino acid sequence....
6.5K
Protein Networks
4.0K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.0K


