| Title: |
alchemlyb: the simple alchemistry library |
| Authors: |
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 |
| Contributors: |
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 |
| Publication Year: |
2024 |
| Collection: |
Università degli studi di Trieste: ArTS (Archivio della ricerca di Trieste) |
| Subject Terms: |
software; alchemical free energy calculations |
| Description: |
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. 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 computationalchemistry specialists, to use alchemlyb effectively. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| Relation: |
volume:9; issue:101; firstpage:-; lastpage:-; numberofpages:8; journal:JOURNAL OF OPEN SOURCE SOFTWARE; https://hdl.handle.net/11368/3101644; https://joss.theoj.org/papers/10.21105/joss.06934 |
| DOI: |
10.21105/joss.06934 |
| Availability: |
https://hdl.handle.net/11368/3101644; https://doi.org/10.21105/joss.06934; https://joss.theoj.org/papers/10.21105/joss.06934 |
| Rights: |
info:eu-repo/semantics/openAccess ; license:Creative commons ; license uri:http://creativecommons.org/licenses/by/4.0/ |
| Accession Number: |
edsbas.6B3499E5 |
| Database: |
BASE |