在极地和非极地溶剂中解决宏循环符合性采样的挑战:为化特征的教训
Xuechen Tang1, Janik Kokot1, Franz Waibl1,2
1Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, A-6020 Innsbruck, Austria.
Journal of chemical information and modeling
|November 9, 2023
概括
这项研究提供了一个强大的工作流程,用于采样使用加速分子动态的基宏循环构造. 该方法在极性溶剂中表现有前途,但对于 хлороформ等非极性溶剂需要仔细的参数化.
科学领域:
- 计算化学是一种计算化学.
- 分子建模分子建模
- 药物发现 药物发现
背景情况:
- 类宏循环在药物发现中很重要.
- 由于高能量障碍,对它们的构造空间进行采样具有挑战性.
研究的目的:
- 评估工作流程,以获得可靠的性宏循环的构造样本.
- 评估工作流在不同溶剂环境中的性能.
主要方法:
- 使用加速分子动力学 (aMD) 模拟.
- 从SMILES字符串开始生成初始结构.
- 研究了部分电荷和质子化状态的影响.
主要成果:
- 工作流在极性溶剂 (水,DMSO) 中表现良好.
- 合金中的合规组合对部分电荷选择敏感.
- 质子状态对形状组合的影响最小.
结论:
- 开发的工作流可靠地采样极性溶剂中的宏循环构造.
- 无极溶剂模拟需要仔细选择参数,特别是部分电荷.
- 准确的形状采样对于预测膜透和宏观循环的特性至关重要.
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