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alchemlyb:简单的炼金术库。

alchemlyb: the simple alchemistry library.

作者信息

Wu Zhiyi, Dotson David L, Alibay Irfan, Allen Bryce K, Barhaghi Mohammad Soroush, Hénin Jérôme, Joseph Thomas T, Kenney Ian M, Lee Hyungro, Li Haoxi, Lim Victoria, Liu Shuai, Marson Domenico, Merz Pascal T, Schlaich Alexander, Mobley David, Shirts Michael R, Beckstein Oliver

机构信息

Exscientia plc, Schroedinger Building, Oxford, United Kingdom.

Department of Physics, Arizona State University, Tempe, Arizona, United States of America.

出版信息

J Open Source Softw. 2024;9(101). doi: 10.21105/joss.06934. Epub 2024 Sep 26.

Abstract

is an open-source Python software package for the analysis of alchemical free energy calculations, an important method in computational chemistry and biology, most notably in the field of drug discovery (Merz et al., 2010). Its functionality contains individual composable building blocks for all aspects of a full typical free energy analysis workflow, starting with the extraction of raw data from the output of diverse molecular simulation packages, moving on to data preprocessing tasks such as decorrelation of time series, using various estimators to derive free energy estimates from simulation samples, and finally providing quality analysis tools for data convergence checking and visualization. also contains high-level end-to-end workflows that combine multiple building blocks into a user-friendly analysis pipeline from the initial data input stage to the final results. This workflow functionality enhances accessibility by enabling researchers from diverse scientific backgrounds, and not solely computational chemistry specialists, to use effectively.

摘要

是一个用于分析炼金术自由能计算的开源Python软件包,这是计算化学和生物学中的一种重要方法,在药物发现领域尤为突出(Merz等人,2010年)。其功能包含完整典型自由能分析工作流程各个方面的单个可组合构建块,从从各种分子模拟软件包的输出中提取原始数据开始,接着进行诸如时间序列去相关等数据预处理任务,使用各种估计器从模拟样本中得出自由能估计值,最后提供用于数据收敛检查和可视化的质量分析工具。 还包含高级端到端工作流程,这些工作流程将多个构建块从初始数据输入阶段到最终结果组合成一个用户友好的分析管道。这种工作流程功能通过使来自不同科学背景的研究人员(而不仅仅是计算化学专家)能够有效使用 ,从而提高了可及性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/056a/12352497/56aade28cb37/nihms-2046776-f0001.jpg

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