JOSS paper

.github/workflows/draft-pdf.yml

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+name: JOSS paper build
+
+on: [push]
+
+jobs:
+ paper:
+ runs-on: ubuntu-latest
+ name: Paper Draft
+ steps:
+ - name: Checkout
+ uses: actions/checkout@v4
+ - name: Build draft PDF
+ uses: openjournals/openjournals-draft-action@master
+ with:
+ journal: joss
+ # This should be the path to the paper within your repo.
+ paper-path: joss_paper/paper.md
+ - name: Upload
+ uses: actions/upload-artifact@v4
+ with:
+ name: paper
+ # This is the output path where Pandoc will write the compiled
+ # PDF. Note, this should be the same directory as the input
+ # paper.md
+ path: joss_paper/paper.pdf

joss_paper/paper.bib

@@ -0,0 +1,320 @@
+@article{bennett1976efficient,
+ title={Efficient estimation of free energy differences from Monte Carlo data},
+ author={Bennett, C. H.},
+ journal={Journal of Computational Physics},
+ volume={22},
+ number={2},
+ pages={245-268},
+ year={1976},
+ doi={10.1016/0021-9991(76)90078-4},
+}
+
+
+@article{Case2005uq,
+ author = {Case, David A and Cheatham, 3rd, Thomas E and Darden, Tom and Gohlke, Holger and Luo, Ray and Merz, Jr, Kenneth M and Onufriev, Alexey and Simmerling, Carlos and Wang, Bing and Woods, Robert J},
+ journal = {J Comput Chem},
+ number = {16},
+ pages = {1668-1688},
+ title = {The {Amber} biomolecular simulation programs},
+ volume = {26},
+ year = {2005},
+ doi = {10.1002/jcc.20290}
+}
+
+
+@article{chodera2007use,
+ title={Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations},
+ author={J. D. Chodera and Swope, W. C. and Pitera, J. W. and Seok, C. and Dill, K. A.},
+ journal={J Chem Theory Comput},
+ volume={3},
+ number={1},
+ pages={26-41},
+ year={2007},
+ doi={10.1021/ct0502864},
+}
+
+
+@article{Nejahi2021aa,
+ author = {Younes Nejahi and Mohammad Soroush Barhaghi and Gregory Schwing and Loren Schwiebert and Jeffrey Potoff},
+ journal = {SoftwareX},
+ pages = {100627},
+ title = {Update 2.70 to ``{GOMC}: {GPU} Optimized {Monte Carlo} for the simulation of phase equilibria and physical properties of complex fluids''},
+ volume = {13},
+ doi = {10.1016/j.softx.2020.100627},
+ year = {2021}
+}
+
+
+@article{deng2009computations,
+ title={Computations of standard binding free energies with molecular dynamics simulations},
+ author={Deng, Y. and Roux, B.},
+ journal={J Phys Chem B},
+ volume={113},
+ number={8},
+ pages={2234-2246},
+ year={2009},
+ doi={10.1021/jp807701h},
+}
+
+@article{gusev2023active,
+ title={Active Learning Guided Drug Design Lead Optimization Based on Relative Binding Free Energy Modeling},
+ author={Gusev, F. and Gutkin, E. and Kurnikova, M. G. and Isayev, O.},
+ journal={Journal of Chemical Information and Modeling},
+ volume={63},
+ number={2},
+ pages={583-594},
+ year={2023},
+ doi={10.1021/acs.jcim.2c01052},
+}
+
+
+@article{Hedges2019aa,
+ author = {Lester O. Hedges and Antonia S.J.S. Mey and Charles A. Laughton and Francesco L. Gervasio and Adrian J. Mulholland and Christopher J. Woods and Julien Michel},
+ journal = {Journal of Open Source Software},
+ keywords = {free energy, framework, python, MD SIMULATION},
+ number = {43},
+ pages = {1831},
+ publisher = {The Open Journal},
+ title = {{BioSimSpace}: An interoperable {Python} framework for biomolecular simulation},
+ volume = {4},
+ year = {2019},
+ doi = {10.21105/joss.01831}
+}
+
+@article{kirkwood1935statistical,
+ title={Statistical mechanics of fluid mixtures},
+ author={Kirkwood, J. G.},
+ journal={The Journal of Chemical Physics},
+ volume={3},
+ number={5},
+ pages={300-313},
+ year={1935},
+ doi={10.1063/1.1749657},
+}
+
+@article{klimovich2015guidelines,
+ title={Guidelines for the analysis of free energy calculations},
+ author={Klimovich, P. V. and Shirts, M. R. and Mobley, D. L.},
+ journal={J Comput Aided Mol Des},
+ volume={29},
+ number={5},
+ pages={397-411},
+ year={2015},
+ doi={10.1007/s10822-015-9840-9},
+}
+
+@book{merz2010drug,
+ title={Drug design: structure-and ligand-based approaches},
+ author={Merz, Jr, K. M. and Ringe, D. and Reynolds, C. H.},
+ year={2010},
+ publisher={Cambridge University Press},
+}
+
+@article{paliwal2011benchmark,
+ title={A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods},
+ author={Paliwal, H. and Shirts, M. R.},
+ journal={J Chem Theory Comput},
+ volume={7},
+ number={12},
+ pages={4115-4134},
+ year={2011},
+ doi={10.1021/ct2003995},
+}
+
+@article{pham2011identifying,
+ title={Identifying low variance pathways for free energy calculations of molecular transformations in solution phase},
+ author={Pham, T. T. and Shirts, M. R.},
+ journal={J Chem Phys},
+ volume={135},
+ number={3},
+ pages={034114},
+ year={2011},
+ doi={10.1063/1.3607597},
+}
+
+@article{phillips2020scalable,
+ title={Scalable molecular dynamics on CPU and GPU architectures with NAMD},
+ author = {Phillips,James C. and Hardy,David J. and Maia,Julio D. C. and Stone,John E. and Ribeiro,Jo{\~a}o V. and Bernardi,Rafael C. and Buch,Ronak and Fiorin,Giacomo and H{\'e}nin,J{\'e}r{\^o}me and Jiang,Wei and McGreevy,Ryan and Melo,Marcelo C. R. and Radak,Brian K. and Skeel,Robert D. and Singharoy,Abhishek and Wang,Yi and Roux,Beno{\^\i}t and Aksimentiev,Aleksei and Luthey-Schulten,Zaida and Kal{\'e},Laxmikant V. and Schulten,Klaus and Chipot,Christophe and Tajkhorshid,Emad},
+ journal={The Journal of Chemical Physics},
+ volume={153},
+ number={4},
+ pages={044130},
+ year={2020},
+ doi={10.1063/5.0014475},
+}
+
+@article{pohorille2010good,
+ title={Good practices in free-energy calculations},
+ author={Pohorille, A. and Jarzynski, C. and Chipot, C.},
+ journal={J Phys Chem B},
+ volume={114},
+ number={32},
+ pages={10235-10253},
+ year={2010},
+ doi={10.1021/jp102971x},
+}
+
+
+@article{Abraham2015aa,
+ author = {Abraham, Mark James and Murtola, Teemu and Schulz, Roland and P{\'a}ll, Szil{\'a}rd and Smith, Jeremy C. and Hess, Berk and Lindahl, Erik},
+ journal = {SoftwareX},
+ pages = {19 - 25},
+ title = {{GROMACS}: High performance molecular simulations through multi-level parallelism from laptops to supercomputers},
+ volume = {1--2},
+ year = {2015},
+ doi = {10.1016/j.softx.2015.06.001}
+}
+
+@article{shirts2008statistically,
+ title={Statistically optimal analysis of samples from multiple equilibrium states},
+ author={Shirts, M. R. and Chodera, J. D.},
+ journal={J Chem Phys},
+ volume={129},
+ number={12},
+ pages={124105},
+ year={2008},
+ doi={10.1063/1.2978177},
+}
+
+@article{yang2004free,
+ title={Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence},
+ author={Yang, W. and Bitetti-Putzer, R. and Karplus, M.},
+ journal={J Chem Phys},
+ volume={120},
+ number={6},
+ pages={2618-2628},
+ year={2004},
+ doi={10.1063/1.1638996},
+}
+
+@article{zwanzig1954high,
+ title={High‐temperature equation of state by a perturbation method. I. Nonpolar gases},
+ author={Zwanzig, R. W.},
+ journal={The Journal of Chemical Physics},
+ volume={22},
+ number={8},
+ pages={1420-1426},
+ year={1954},
+ doi={10.1063/1.1740409},
+}
+
+@article{fan2020aa,
+ author = {Fan, Shujie and Iorga, Bogdan I. and Beckstein, Oliver},
+ journal = {Journal of Computer-Aided Molecular Design},
+ pages = {543--560},
+ title = {Prediction of octanol-water partition coefficients for the {SAMPL6}-{$\log P$} molecules using molecular dynamics simulations with {OPLS-AA}, {AMBER} and {CHARMM} force fields},
+ volume = {34},
+ year = {2020},
+ doi = {10.1007/s10822-019-00267-z}
+}
+
+
+@article{Mey2020aa,
+ author = {Antonia S. J. S. Mey and Bryce Allen and Hannah E. Bruce Macdonald and John D. Chodera and Maximilian Kuhn and Julien Michel and David L. Mobley and Levi N. Naden and Samarjeet Prasad and Andrea Rizzi and Jenke Scheen and Michael R. Shirts and Gary Tresadern and Huafeng Xu},
+ journal = {Living Journal of Computational Molecular Science},
+ number = {1},
+ pages = {18378},
+ title = {Best Practices for Alchemical Free Energy Calculations},
+ volume = {2},
+ year = {2020},
+ doi = {10.33011/livecoms.2.1.18378} 
+}
+
+
+@article{Chodera2016aa,
+ author = {J. D. Chodera},
+ journal = {Journal of Chemical Theory and Computation},
+ month = {Apr},
+ number = {4},
+ pages = {1799--1805},
+ title = {A Simple Method for Automated Equilibration Detection in Molecular Simulations},
+ volume = {12},
+ year = {2016},
+ doi = {10.1021/acs.jctc.5b00784}
+}
+
+@InProceedings{ mckinney-proc-scipy-2010,
+ author = { {W}es {M}c{K}inney },
+ title = { {D}ata {S}tructures for {S}tatistical {C}omputing in {P}ython },
+ booktitle = { {P}roceedings of the 9th {P}ython in {S}cience {C}onference },
+ pages = { 56 - 61 },
+ year = { 2010 },
+ editor = { {S}t\'efan van der {W}alt and {J}arrod {M}illman },
+ doi = { 10.25080/Majora-92bf1922-00a }
+}
+
+
+@article{scikitlearn2011,
+ title={Scikit-learn: Machine Learning in {P}ython},
+ author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
+ and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
+ and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
+ Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
+ journal={Journal of Machine Learning Research},
+ volume={12},
+ pages={2825--2830},
+ year={2011}
+}
+
+@inproceedings{sklearn2013api,
+ author = {Lars Buitinck and Gilles Louppe and Mathieu Blondel and
+ Fabian Pedregosa and Andreas Mueller and Olivier Grisel and
+ Vlad Niculae and Peter Prettenhofer and Alexandre Gramfort
+ and Jaques Grobler and Robert Layton and Jake VanderPlas and
+ Arnaud Joly and Brian Holt and Ga{\"{e}}l Varoquaux},
+ title = {{API} design for machine learning software: experiences from the scikit-learn
+ project},
+ booktitle = {ECML PKDD Workshop: Languages for Data Mining and Machine Learning},
+ year = {2013},
+ pages = {108--122},
+}
+
+
+@incollection{Schlaich2015aa,
+ address = {J{\"u}lich},
+ author = {Schlaich, A and Kowalik, B and Kandu{\v{c}}, M and Schneck, Emanuel and Netz, RR},
+ booktitle = {Computational Trends in Solvation and Transport in Liquids-Lecture Notes (IAS Series 28)},
+ editor = {Sutmann, G. and Grotendorst, J. and Gompper, G. and Marx, D.},
+ pages = {155--185},
+ publisher = {Forschungszentrum J{\"u}lich GmbH},
+ title = {Simulation techniques for solvation-induced surface-interactions at prescribed water chemical potential},
+ volume = 28,
+ year = 2015
+}
+
+
+@article{Thompson2022aa,
+ author = {Aidan P. Thompson and H. Metin Aktulga and Richard Berger and Dan S. Bolintineanu and W. Michael Brown and Paul S. Crozier and Pieter J. {in 't Veld} and Axel Kohlmeyer and Stan G. Moore and Trung Dac Nguyen and Ray Shan and Mark J. Stevens and Julien Tranchida and Christian Trott and Steven J. Plimpton},
+ journal = {Computer Physics Communications},
+ pages = 108171,
+ title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
+ volume = 271,
+ year = 2022,
+ doi = {10.1016/j.cpc.2021.108171},
+}
+
+
+@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}
+}