alchemlyb: the simple alchemistry library. Wu, Z., Dotson, D. L., Alibay, I., Allen, B. K., Barhaghi, M. S., Hénin, J., Joseph, T. T., Kenney, I. M., Lee, H., Li, H., Lim, V., Liu, S., Marson, D., Merz, P. T., Schlaich, A., Mobley, D., Shirts, M. R., & Beckstein, O. Journal of Open Source Software, 9(101):6934, September, 2024. ![alchemlyb: the simple alchemistry library [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex alchemlyb 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. alchemlyb 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 alchemlyb effectively
@article{wu_alchemlyb_2024,
title = {alchemlyb: the simple alchemistry library},
volume = {9},
issn = {2475-9066},
shorttitle = {alchemlyb},
url = {https://joss.theoj.org/papers/10.21105/joss.06934},
doi = {10.21105/joss.06934},
abstract = {alchemlyb 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. alchemlyb 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 alchemlyb effectively},
language = {en},
number = {101},
urldate = {2024-09-26},
journal = {Journal of Open Source Software},
author = {Wu, Zhiyi and Dotson, David L. and Alibay, Irfan and Allen, Bryce K. and Barhaghi, Mohammad Soroush and Hénin, Jérôme and Joseph, Thomas T. and Kenney, Ian M. and Lee, Hyungro and Li, Haoxi and Lim, Victoria and Liu, Shuai and Marson, Domenico and Merz, Pascal T. and Schlaich, Alexander and Mobley, David and Shirts, Michael R. and Beckstein, Oliver},
month = sep,
year = {2024},
pages = {6934},
}
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Its functionality contains individual composable\nbuilding blocks for all aspects of a full typical free energy analysis workflow, starting with the\nextraction of raw data from the output of diverse molecular simulation packages, moving on to\ndata preprocessing tasks such as decorrelation of time series, using various estimators to derive\nfree energy estimates from simulation samples, and finally providing quality analysis tools for\ndata convergence checking and visualization. alchemlyb also contains high-level end-to-end\nworkflows that combine multiple building blocks into a user-friendly analysis pipeline from the\ninitial data input stage to the final results. 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