标准约束性自由能源计算:我们离自动化还有多远?
Haohao Fu1,2, Christophe Chipot3,4,5,6, Xueguang Shao1,2
1State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Center for Analytical Sciences, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China.
The journal of physical chemistry. B
|October 12, 2023
概括
为了更广泛的采用,自动化蛋白质 - 配体结合的自由能量计算至关重要. 最近在自适应算法和用户友好的软件方面的进展为更容易获得的计算药物发现铺平了道路.
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:
- 在in silico蛋白质 - 配体结合的自由能量计算接近化学准确度.
- 由于人类的重大干预,特别是对于新用户而言,广泛应用受到阻碍.
- 自动化对于克服这些局限性和实现更广泛的使用至关重要.
研究的目的:
- 审查自动化具有约束力的自由能计算标准的进展情况.
- 评估自动化方法的现状和局限性.
- 概述对增强自动化的未来要求.
主要方法:
- 对自适应和无参数算法的讨论.
- 具有约束力的自由能量计算工作流程的标准化.
- 实现用于计算化学的用户友好的软件.
主要成果:
- 在自动化关键的人力工作方面取得了重大进展,在具有约束力的自由能源计算方面取得了重大进展.
- 适应性和无参数算法减少了手动调整的需要.
- 标准化工作流程和用户友好的软件正在出现.
结论:
- 自动化工作流程对于民主化in silico结合亲和度估计至关重要.
- 需要进一步开发以解决局限性并支持多样化的蛋白质-连接体系统.
- 未来的算法必须优先考虑易用性和最小的用户输入.
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