CSMILES:一个紧的,人类可读的SMILES扩展用于形状的扩展
James W Furness1, Kevin B Moore1, Art Bochevarov1
1Schrödinger, Inc., 1540 Broadway, Floor 24, New York, New York 10036, United States.
Journal of chemical information and modeling
|September 26, 2025
概括
一个新的化学符号,Conformer-SMILES (CSMILES),编码分子3D结构和二面角在紧的字符串. 这种方法允许对分子对应物的规范表示,不变于旋转和转换,从而实现高效的数据存储和机器学习应用.
科学领域:
- 计算化学的计算化学
- 化学信息学 化学信息学
- 结构生物学 结构生物学
背景情况:
- 像SMILES这样的现有分子线符号方案缺乏区分同一分子的各种构造的能力.
- 高效地表示和存储3D分子结构对于计算化学和药物发现至关重要.
研究的目的:
- 开发SMILES符号的扩展,称为CSMILES,能够编码特定的分子调整器信息.
- 为3D分子结构创建一个紧和正规的基于文本的表示,包括二面角.
主要方法:
- CSMILES扩展了标准的SMILES,将二面角值直接纳入字符串内的键符.
- 符合水平的规范化确保了原子重新排序,转换和旋转的不变性.
- 在3D结构和CSMILES之间实现了一种双向转换工具,由Python代码支持.
主要成果:
- CSMILES字符串提供了一个紧而可读的分子对应物的表示,即使是涉及分支,环和对称性的复杂结构.
- 规范的CSMILES字符串对常见的转换是不变的,确保一致的表示.
- 一个功能性的 Python 实现方便了在 3D 分子数据和 CSMILES 符号之间进行转换.
结论:
- CSMILES提供了一种新且高效的方法来表示和存储3D分子结构信息.
- 开发的符号在开发机器学习模型中具有潜在的应用,用于依赖形状的分子性质.
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