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joss_paper/paper.md

@@ -41,16 +41,16 @@ A distinctive attribute of *alchemlyb* is its streamlined, end-to-end analysis w
 
 # Statement of need
 
-In the pharmaceutical sector, computational chemistry techniques are integral for evaluating potential drug compounds based on their protein binding affinity [@deng2009computations]. Notably, absolute binding free energy calculations between proteins and ligands or relative binding affinity of ligands to the same protein are routinely employed for this purpose [@merz2010drug]. The resultant estimates of these free energies are essential for understanding binding affinity throughout various stages of drug discovery, such as hit identification and lead optimization [@merz2010drug]. Other free energies extracted from simulations are useful in solution thermodynamics, chemical engineering, environmental science, and material science. The *alchemlyb* software processes the raw data from MD simulations using key estimators from statistical mechanics, drastically simplifying the process of extracting crucial thermodynamic insights from molecular simulations [^1].
-
-[^1]: As of 29/12/2023, *alchemlyb* has been downloaded 23,922 times from [conda-forge](https://anaconda.org/conda-forge/alchemlyb/files).
+In the pharmaceutical sector, computational chemistry techniques are integral for evaluating potential drug compounds based on their protein binding affinity [@deng2009computations]. Notably, absolute binding free energy calculations between proteins and ligands or relative binding affinity of ligands to the same protein are routinely employed for this purpose [@merz2010drug]. The resultant estimates of these free energies are essential for understanding binding affinity throughout various stages of drug discovery, such as hit identification and lead optimization [@merz2010drug]. Other free energies extracted from simulations are useful in solution thermodynamics, chemical engineering, environmental science, and material science. The *alchemlyb* software processes the raw data from MD simulations using key estimators from statistical mechanics, drastically simplifying the process of extracting crucial thermodynamic insights from molecular simulations .
 
 Various molecular dynamics (MD) engines, including GROMACS [@pronk2013gromacs], AMBER [@case2014ff14sb], GOMC [@cummings2021open], and NAMD [@phillips2020scalable], offer distinct tools for performing free energy calculations. However, the diversity in output formats and analysis tools among different MD engines complicates the research process. Data generated by each engine requires individualized processing and analysis methods, hindering seamless collaboration and comparison of results.
 
 
 THe [alchemical-analysis.py](https://github.com/MobleyLab/alchemical-analysis) tool [@klimovich2015guidelines], which preceeded *alchemlyb*, addressed this problem. Now that [alchemical-analysis.py](https://github.com/MobleyLab/alchemical-analysis) has been deprecated, *alchemlyb* continues to provide a unified, engine-agnostic analysis workflow. Unlike its predecessor, *alchemlyb* breaks down components of the workflow into modular tools, allowing users to more easily customize their analysis. This innovation enables consistent processing of free energy data from diverse MD engines, facilitating streamlined comparison and combination of results.
 
-Notably, *alchemlyb*'s robust and user-friendly nature has led to its integration into other automated workflow libraries such as BioSimSpace [@hedges2023suite]. This further enhances its accessibility and usability within broader scientific workflows, reinforcing its position as a versatile and essential tool in the field of computational chemistry.
+Notably, *alchemlyb*'s robust and user-friendly nature has led to its integration into other automated workflow libraries such as BioSimSpace [@hedges2023suite]. This further enhances its accessibility and usability within broader scientific workflows, reinforcing its position as a versatile and essential tool in the field of computational chemistry [^1].
+
+[^1]: As of 29/12/2023, *alchemlyb* has been downloaded 23,922 times from [conda-forge](https://anaconda.org/conda-forge/alchemlyb/files).
 
 # Implementation
 
@@ -68,7 +68,7 @@ To evaluate the accuracy of the free energy estimate, *alchemlyb* offers a range
 
 # Acknowledgements
 
-O.B. and D.D. designed the project. Z.W., D.D., contribute to the new features. Z.W., D.D., O.B. maintain the codebase. Z.W. and M.R.S wrote the manuscript.
+O.B. and D.D. designed the project. Z.W., D.D., contribute to the new features. Z.W., D.D., O.B. maintain the codebase. Z.W., M.R.S wrote the manuscript.
 
 # References