alchemlyb: the simple alchemistry library
<i>alchemlyb</i> 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. <i>alchemlyb</i> 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 <i>alchemlyb</i> effectively.
Authors
- Bryce K. Allen (ORCID: https://orcid.org/0000-0002-0804-8127)
- David L. Mobley (ORCID: https://orcid.org/0000-0002-1083-5533)
- Hyungro Lee (ORCID: https://orcid.org/0000-0002-4221-7094)
- Ian M. Kenney (ORCID: https://orcid.org/0000-0002-9749-8866)
- Jérôme Hénin (ORCID: https://orcid.org/0000-0003-2540-4098)
- Zhiyi Wu (ORCID: https://orcid.org/0000-0002-7615-7851)
- Irfan Alibay (ORCID: https://orcid.org/0000-0001-5787-9130)
- Mohammad Soroush Barhaghi (ORCID: https://orcid.org/0000-0001-8226-7347)
- Oliver Beckstein (ORCID: https://orcid.org/0000-0003-1340-0831)
- Domenico Marson (ORCID: https://orcid.org/0000-0003-1839-9868)
- David Dotson (ORCID: https://orcid.org/0000-0001-5879-2942)
- Victoria T. Lim (ORCID: https://orcid.org/0000-0003-4030-9312)
- Thomas T. Joseph (ORCID: https://orcid.org/0000-0003-1323-3244)
- Michael R. Shirts (ORCID: https://orcid.org/0000-0003-3249-1097)
- Alexander Schlaich (ORCID: https://orcid.org/0000-0002-4250-363X)
- Pascal T. Merz (ORCID: https://orcid.org/0000-0002-7045-8725)
- Haoxi Li (ORCID: https://orcid.org/0009-0004-8369-1042)
- S. Liu (ORCID: https://orcid.org/0000-0002-8632-633X)
Institutions
- University of Stuttgart (DE)
- University of North Carolina at Chapel Hill (US)
- Centre National de la Recherche Scientifique (FR)
- University of North Carolina Health Care (US)
- University of Trieste (IT)
- Pacific Northwest National Laboratory (US)
- Wayne State University (US)
- University of Colorado Boulder (US)
- University of California, Irvine (US)
- Université Paris Cité (FR)
- Oxford University Press (United Kingdom) (GB)
- Open Geospatial Consortium (US)
- Laboratoire de Biochimie Théorique (FR)
- Silicon Therapeutics (United States) (US)
- Mirati Therapeutics (United States) (US)
- Institut de Biologie Physico-Chimique (FR)
- Scientific Consulting Group (US)
- Irvine University (US)
- Ping (United States) (US)
- University of North Carolina System (US)
- Arizona State University (US)
- University of Pennsylvania (US)
Publication Details
- Journal
- The Journal of Open Source Software
- Published
- 2024-09-26
- DOI
- https://doi.org/10.21105/joss.06934
- Citations
- 24
- Primary Topic
- Various Chemistry Research Topics
- Type
- article
- Field-Weighted Citation Impact
- 9.79
Funders
- National Science Foundation
- Deutsche Forschungsgemeinschaft
- National Institutes of Health
- Singapore Institute of Manufacturing Technology