Add JH to author lists, extra reference (#365)

* Add mention of SAFEP * Add JH to author list, first SAFEP reference also reorder middle authors alphabetically. --------- Co-authored-by: Tom Joseph <[email protected]>
alchemistry · May 28, 2024 · 1f01ec7 · 1f01ec7
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diff --git a/joss_paper/paper.bib b/joss_paper/paper.bib
@@ -288,3 +288,29 @@ @article{Thompson2022aa
 	volume = 271,
 	year = 2022
 }
+
+
+@Article{Salari2018,
+  author       = {Salari, Reza and Joseph, Thomas and Lohia, Ruchi and Hénin, Jérôme and Brannigan, Grace},
+  title        = {A Streamlined, General Approach for Computing Ligand Binding Free Energies and Its Application to GPCR-Bound Cholesterol.},
+  journal      = {Journal of Chemical Theory and Computation},
+  year         = {2018},
+  volume       = {14},
+  number       = {12},
+  pages        = {6560--6573},
+  doi          = {10.1021/acs.jctc.8b00447},
+}
+
+
+@article{santiagomcrae2023,
+    author={Santiago-McRae, E., and Ebrahimi, M. and Sandberg, J. W. and Brannigan, G. and Hénin, J.},
+    title={Computing Absolute Binding Affinities by Streamlined Alchemical Free Energy Perturbation (SAFEP) [Article v1.0]},
+    url={https://livecomsjournal.org/index.php/livecoms/article/view/v5i1e2067},
+    doi={10.33011/livecoms.5.1.2067}, 
+    journal={Living Journal of Computational Molecular Science}, 
+    year={2023}, 
+    month={Oct.},
+    volume={5}, 
+    number={1}, 
+    pages={2067}
+}
diff --git a/joss_paper/paper.md b/joss_paper/paper.md
@@ -14,24 +14,27 @@ authors:
     orcid: 0000-0001-5879-2942
     equal-contrib: true
     affiliation: "2, 3"
-  - name: Domenico Marson
-    orcid: 0000-0003-1839-9868
-    affiliation: 6
+  - name: Jérôme Hénin
+    orcid: 0000-0003-2540-4098
+    affiliation: 4
   - name: Thomas T. Joseph
     orcid: 0000-0003-1323-3244
-    affiliation: 7
+    affiliation: 5
   - name: Haoxi Li
     orcid: 0009-0004-8369-1042
-    affiliation: 8
+    affiliation: 6
+  - name: Domenico Marson
+    orcid: 0000-0003-1839-9868
+    affiliation: 7
   - name: Alexander Schlaich
     orcid: 0000-0002-4250-363X
-    affiliation: 9
+    affiliation: 8
   - name: David Mobley
     orcid: 0000-0002-1083-5533
-    affiliation: 4	
+    affiliation: 9
   - name: Michael R. Shirts
     orcid: 0000-0003-3249-1097
-    affiliation: 5
+    affiliation: 10
   - name: Oliver Beckstein
     orcid: 0000-0003-1340-0831
     corresponding: true
@@ -43,19 +46,21 @@ affiliations:
    index: 2
  - name: Datryllic LLC, Phoenix, Arizona, USA (present affiliation)
    index: 3
- - name: University of California Irvine, Irvine, California, USA
+ - name: Université Paris Cité, CNRS, Laboratoire de Biochimie Théorique, Paris, France
    index: 4
- - name: University of Colorado Boulder, Boulder, Colorado, USA
+ - name: Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
    index: 5
- - name: Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Trieste, Italy
+ - name: UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
    index: 6
- - name: Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
+ - name: Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTS), DEA, University of Trieste, Trieste, Italy
    index: 7
- - name: UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA.
-   index: 8 
-
  - name: Stuttgart Center for Simulation Science (SC SimTech) & Institute for Computational Physics, University of Stuttgart, 70569 Stuttgart, Germany 
+   index: 8
+ - name: University of California Irvine, Irvine, California, USA
    index: 9
+ - name: University of Colorado Boulder, Boulder, Colorado, USA
+   index: 10
+
 date: 31 May 2024
 bibliography: paper.bib
 
@@ -158,6 +163,8 @@ For statistical validity, the accumulated samples should be collected from equil
 ## Workflows
 
 The building blocks are sufficient to compute free energies from alchemical free energy simulations and assess their reliability.
+This functionality is used, for example, by the Streamlined Alchemical Free Energy Perturbation (SAFEP) analysis scripts [@Salari2018; @santiagomcrae2023].
+
 *alchemlyb* also provides a structure to combine the building blocks into full end-to-end workflows (module `alchemlyb.workflows`).
 As an example, the `ABFE` workflow for absolute binding free energy estimation reads in the raw input data and performs decorrelation, estimation, and quality plotting of the estimate.
 It can directly estimate quantities such as solvation free energies and makes it easy to calculate more complex quantities such as absolute binding free energies (as the difference between the solvation free energy of the ligand in water and the solvation free energy of the ligand in the protein's binding pocket).