尼莫:一种基于条件变压器的自然产品灵感分子生成模型
Xiaojuan Shen1, Tao Zeng1, Nianhang Chen1
1School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
Molecules (Basel, Switzerland)
|April 27, 2024
概括
我们开发了NIMO,这是一种使用变压器神经网络的计算工具,用于扩大天然产品的化学多样性,用于药物发现. 尼莫在产生新型分子和优化现有结构方面表现出色.
科学领域:
- 药用化学 医学化学
- 计算机化药物发现技术
- 人工智能在药物设计中的应用
背景情况:
- 自然产品 (NPs) 对于药物发现至关重要,因为它们具有多样化的生物活动和结构复杂性.
- 扩大NP的化学空间对于识别新疗法至关重要.
- 目前的NP勘探方法在获取新型化学支架方面存在局限性.
研究的目的:
- 介绍NIMO,一种用于生成和优化自然产品类分子的新型计算工具.
- 利用变压器神经网络和图案提取来增强分子生成.
- 探索NIMO在各种分子生成任务中的能力,包括结构导向和活动导向设计.
主要方法:
- 开发NIMO,一个基于变压器神经网络的计算工具.
- 实施两种定制的图案提取方法,将分子图形转换为语义图案序列.
- 在各种任务场景下使用NIMO生成的图案序列培训分子生成模型.
- 评估NIMO在结构导向,活动导向和基于口袋的分子生成方面的表现.
主要成果:
- 在生成 de novo (从零开始) 的分子方面,NIMO表现出色.
- 该工具在优化基于给定的支架的分子结构方面表现出高效.
- 尼莫成功地识别了用于有效分子生成的语法模式和结构属性关系.
结论:
- 尼莫代表了自然产品药物发现计算方法的重大进步.
- 该工具有效地扩大了天然产品的可访问化学空间.
- 通过高效的分子生成和优化,NIMO显示出加速新药候选物识别的前景.
相关概念视频
Synthetic Biology
4.7K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
4.7K
Transformers
1.1K
A device that transforms voltages from one value to another using induction is called a transformer. A transformer consists of two separate coils, or windings, wrapped around the same soft iron core. However, they are electrically insulated from each other.
The iron core has a substantial relative permeability. Therefore, the magnetic field lines generated due to the current in one winding are almost entirely confined within the core, such that the same magnetic flux permeates each turn of both...
The iron core has a substantial relative permeability. Therefore, the magnetic field lines generated due to the current in one winding are almost entirely confined within the core, such that the same magnetic flux permeates each turn of both...
1.1K
Molecular Models
38.3K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
38.3K
Predicting Products: SN1 vs. SN2
13.4K
Nucleophilic substitution reactions of alkyl halides can proceed via an SN1 or an SN2 mechanism. While in SN2 reactions, the nucleophile attacks the substrate simultaneously as the leaving group departs, in SN1 reactions, the substrate first dissociates to give the carbocation intermediate. Various factors such as the structure of the substrate, the strength of the nucleophile, and the nature of the solvent promote one mechanism over the other.
With increased substitution on the alkyl halide,...
With increased substitution on the alkyl halide,...
13.4K
Gene Conversion
2.3K
2.3K
Combinatorial Gene Control
8.3K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
8.3K


