Perspective

A Community Letter Regarding Sharing

Bimolecular Simulation Data for COVID-19
Rommie E. Amaro, and Adrian J. Mulholland
J. Chem. Inf. Model., Just Accepted Manuscript • DOI: 10.1021/acs.jcim.0c00319 • Publication Date (Web): 07 Apr 2020
Downloaded from pubs.acs.org on April 15, 2020

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3 Molecular simulation and modelling can contribute to combating the current COVID-19 global
4 pandemic, e.g. helping to identify leads for therapies, diagnostics and vaccines for COVID-19,
5 suggesting potential antiviral drugs, analyzing structural effects of genetic variation in the SARS-
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CoV-2 virus and molecular recognition relevant to protein-protein and protein-inhibitor systems.
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Such efforts complement experiments, can be linked to emerging artificial intelligence (AI)
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methods, and add molecular insight to genetic studies and mathematical models for pandemic
10 risk assessment and predicting the impact of different potential non-pharmaceutical interventions
11 (NPI). To maximize the impact and value of molecular simulation methods in this crisis, we as an
12 international community recognize the need to modify our standard practices to maximize the
13 effectiveness of our global response to the pandemic.
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15 There is an urgent need to share our methods, models, and results openly and quickly to test
16 findings, ensure reproducibility, test significance, eliminate dead-ends, and accelerate discovery.
17 Sharing of data for COVID-19 applications will help connect scientists across the global
18 biomolecular simulation community, and also improve connection and communication between
19 simulation and experimental and clinical data and investigators.
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21 We, as a community, commit to the following principles:
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24  We commit to making results from our work on the SARS-CoV-2 virus available as
25 preprints as quickly as possible, using preprint servers such as arXiv, bioRxiv, and
26 ChemRxiv, and open access data repositories such as Zenodo.
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28  We commit to making available the input files, model building / processing scripts (e.g.
29 Jupyter notebooks) required to set up, run, and analyze the simulations, and data
30 necessary to repeat analysis upon deposition to the preprint sites following the FAIR data
31 principles (findable, accessible, interoperable, reusable) 1. Doing so will also enable others
32 to test, extend and augment developed models without duplicating efforts, delivering
33 results more rapidly, and developing and testing hypotheses.
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35  We will make models and trajectories available as soon as possible through open data
36 sharing platforms such as the Molecular Sciences Software Institute (MolSSI) SARS-CoV-
37 2 Biomolecular Simulation Data and Algorithm Store 2, the Open Science Framework 3,
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and the European Open Science Cloud 4.
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 Where appropriate, we will also share algorithms and methods in order to accelerate reuse
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42 and innovation. Well-validated and functional machine learning methods and heuristic
43 property calculators would be especially desirable, as are Monte Carlo models of
44 infectious disease spread and prediction of the impact of different NPI strategies. Custom
45 code will be made rapidly available in appropriate repositories (e.g., GitHub).
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47  We commit to applying thoughtful permissive (and open source) licensing strategies (such
48 as those recommended by Reproducible Research Standard) 5 to ensure that our models
49 and data can be maximally reused, modified, and redistributed to rapidly advance the field
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1 https://www.nature.com/articles/sdata201618
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2 https://github.com/MolSSI/CoVMME
54 3 https://osf.io
55 4 https://www.eosc-portal.eu
56 5 https://web.stanford.edu/~vcs/talks/VictoriaStoddenCommuniaJune2009-2.pdf
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3 in developing new therapies, while appropriately recognizing and acknowledging original
4 authors and contributors.
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In support of these efforts, the SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store
8 draws on the expertise and discussion of several recent workshops, as well as ongoing
9 community discussions 6,7. The NSF MolSSI has recently created a special call for Seed
10 Fellowship applications for students and postdocs that focus on software development, data
11 science, workflows, and machine learning challenges that are especially relevant to the on-going
12 COVID-19 research. Furthermore, the NSF MolSSI is setting up a centralized github and file
13 sharing service to provide a centralized site for community data, and is also working with Zenodo
8 and the Open Science Grid 9 to help store data and data analysis outcomes for this global
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15 initiative. Our community should be aware of high performance compute resources made
16 available for COVID-19 research (e.g. https://www.ibm.com/ covid19/hpc-consortium).
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18 We recognize that we represent only a cross section of our community, and encourage others to
19 follow these principles; all are welcome to join this effort. We offer our support to others already
20 working on open data efforts in the hope that others working on COVID-19 in biomolecular
21 simulation and other areas will adopt similar best practices.
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24 Signed:
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26 Rommie E. Amaro*, UC San Diego, USA ramaro@ucsd.edu
27 Adrian J. Mulholland*, University of Bristol, UK Adrian.Mulholland@bristol.ac.uk
28 Teresa Head-Gordon, UC Berkeley, USA
29 John D. Chodera, MSKCC, USA
30 Zoe Cournia, Academy of Athens, Greece
31 Vittorio Limongelli, USI Lugano, Switzerland and University of Naples, Italy
32 Shantenu Jha, MolSSI / Rutgers / Brookhaven National Laboratory, USA
33 Marco De Vivo, Italian Institute of Technology, Italy
34 Matteo Dal Peraro, EPFL, Switzerland
35 Andrea Cavalli, U Bologna, Italian Institute of Technology, Italy
36 Alexandre Bonvin, Utrecht University, The Netherlands
37 David Mobley, UC Irvine, USA
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Jean-Philip Piquemal, Sorbonne Université, France
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Pengyu Ren, UT Austin, USA
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Arvind Ramanathan, Argonne National Laboratory/ University of Chicago, USA
42 Lynn Kamerlin, Uppsala University, Sweden
43 Julien Michel, University of Edinburgh, UK
44 Marc van der Kamp, University of Bristol, UK
45 Shozeb Haider, University College London, UK
46 Munir Skaf, University of Campinas, Brazil
47 Adrian Roitberg, U Florida, USA
48 Andrew McCammon, UC San Diego, USA
49 Ivet Bahar, U Pittsburgh, USA
50 Lillian Chong, U Pittsburgh, USA
51 Xuhui Huang, The Hong Kong University of Science and Technology, Hong Kong, China SAR
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53 6 https://pubs.acs.org/doi/full/10.1021/acs.jcim.9b00665
54 7 http://www.hecbiosim.ac.uk/covid-19
55 8 https://zenodo.org/
56 9 https://opensciencegrid.org/
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3 Modesto Orozco, IRB Barcelona, Spain
4 Mark Sansom, University of Oxford, UK
5 Kenneth Merz, Michigan State University, USA
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Chandra Verma, Bioinformatics Institute, A*Star, Singapore
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Makoto Taiji, RIKEN, Japan
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Charlie Laughton, University of Nottingham, UK
10 Paolo Carloni, Juelich Research Center, Germany
11 Francesco Luigi Gervasio, University College London, UK
12 Siewert-Jan Marrink, University of Groningen, The Netherlands
13 Katarzyna Świderek, Universitat Jaume I, Spain
14 Vicent Moliner, Universitat Jaume I, Spain
15 Iñaki Tuñón, Universidad de Valencia, Spain
16 Rebecca Wade, HITS and Heidelberg University, Germany
17 Jonathan Essex, University of Southampton, UK
18 Alessio Lodola, University of Parma, Italy
19 Andre Merzky, RADICAL-Consulting, Germany
20 Charles L. Brooks III, University of Michigan, USA
21 Vincent A. Voelz, Temple University, USA
22 Yuji Sugita, RIKEN, Japan
23 Richard Henchman, University of Manchester, UK
24 Alberto Perez, University of Florida, USA
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Philip Biggin, University of Oxford, UK
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Michele Parrinello, ETH Zurich, Switzerland
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Gregory Voth, U Chicago, USA
29 Adrian Turjanski, University of Buenos Aires, Argentina
30 Marcelo Marti, University of Buenos Aires, Argentina
31 Marina Guenza, University of Oregon, USA
32 Helmut Grubmueller, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
33 William Jorgensen, Yale University, USA
34 David E. Shaw, D. E. Shaw Research and Columbia University, USA
35 Thanyada Rungrotmongkol, Chulalongkorn University, Thailand
36 Supot Hannongbua, Chulalongkorn University, Thailand
37 TJuan R. Perilla, University of Delaware, USA
38 Syma Khalid, University of Southampton, UK
39 Arieh Warshel, University of Southern California, USA
40 Margaret S. Cheung, University of Houston, USA
41 Rosa Di Felice, University of Southern California, USA
42 Carol Parish, University of Richmond, USA
43 Chia-en A. Chang, University of California, Riverside, USA
44 Joanna Trylska, University of Warsaw, Poland
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Zahra Jamshidi, Sharif University of Technology, Tehran, Iran
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Irina Tikhonova, Queen’s University Belfast, UK
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Michelle A. Sahai, University of Roehampton, UK
49 Ana-Nicoleta Bondar, FU Berlin, Germany
50 Anastassia Alexandrova, UCLA, USA
51 Jessica Swanson, University of Utah, USA
52 Leticia F. Cugliandolo, Sorbonne Universite, France
53 Sapna Sarupria, Clemson University, USA
54 Sohail Murad, Illinois Institute of Technology, Chicago, USA
55 Stacey Wetmore, University of Lethbridge, Canada
56 Maria Joao Ramos, University of Porto, Portugal
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3 Mina Yoon, Oak Ridge National Laboratory/University of Tennessee, USA
4 Chris Chipot, CNRS/University of Illinois, USA
5 Cecilia Clementi, Rice University USA/Freie Universitat Berlin, Germany
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Lucie Delemotte, KTH, Sweden
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Adriana Pietropaolo, University of Catanzaro, Italy
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Clemence Corminboeuf, EPFL, Lausanne, Switzerland
10 Matthieu Montes, CNAM, Paris, France
11 Rick Stevens, Argonne National Laboratory/University of Chicago, USA
12 Lyudmila Slipchenko, Purdue University, USA
13 Nadia Elghobashi-Meinhardt, Technische Universität Berlin, Germany
14 Ksenia Bravaya, Boston University, USA
15 Svetlana Malinovskaya, Stevens Institute of Technology, Hoboken, NJ, USA
16 Alessandra Magistrato CNR-IOM at SISSA, Trieste, Italy
17 Jonathan Hirst, University of Nottingham, UK
18 Charlie Catlett, Discovery Partners Institute, Chicago, IL, USA
19 Frank Noé, FU Berlin, Germany
20 Lee-Wei Yang, National Tsing Hua University, Taiwan
21 Shikha Nangia, Syracuse University, USA
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Jana Shen, University of Maryland School of Pharmacy, USA
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Yun Lyna Luo, Western University of Health Sciences, CA, USA
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Theresa Windus, Iowa State University and Ames Laboratory, IA , USA
26 Thereza A. Soares, Federal University of Pernambuco, Brazil
27 Mary Jo Ondrechen, Northeastern University, MA, USA
28 Tamar Schlick, New York University, New York, NY, USA
29 Rebecca Wade, Heidelberg University, Germany
30 Benoît Roux, University of Chicago
31 Sharon Loverde, City University of New York, New York, NY, USA
32 Yongmei Wang, University of Memphis, TN, USA
33 Julia E. Rice, IBM Research - Almaden, CA, USA
34 Irene Yarovsky, RMIT University, Melbourne, Australia
35 Nathalie Reuter, University of Bergen, Norway
36 Leticia Gonzàlez, University of Vienna, Austria
37 Katie Mitchell-Koch, Wichita State University, KS, USA
38 Laura Gagliardi, University of Minnesota, MN, USA
39 Debra J. Bernhardt, The University of Queensland, Australia
40 Marti Head, Oak Ridge National Laboratory/University of Tennessee, Oak RIdge TN USA
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Ruxandra Dima, University of Cincinnati, USA
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George Stan, University of Cincinnati, USA
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Shivangi Nangia, Dickinson State University, USA
45 Peng Tao, Southern Methodist University, Dallas, TX, USA
46 Alexandra Freidzon, Photochemistry Center, Russian Academy of Sciences
47 Feng Wang, Swinburne University of Technology, Australia
48 Hongchun Li, Shenzhen Institutes of Advanced Technology, CAS, China
49 Jin Liu, University of North Texas Health Science Center, Fort Worth, TX
50 Hao Dong, Nanjing University, Nanjing, China
51 Jing Ma, Nanjing University, Nanjing, China
52 Durba Sengupta, NCL-Pune, India
53 Tomasz Borowski, ICSC, Polish Academy of Sciences
54 Rati Sharma, IISER Bhopal, India
55 Vannajan Sanghiran Lee, Malaysia
56 Elisa Fadda, Dublin, Ireland
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3 Christof Jäger, University of Nottingham, UK
4 Malgorzata Biczysko, Shanghai University, China
5 Matej Praprotnik, National Institute of Chemistry, Slovenia
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Anna Croft, University of Nottingham, UK
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Charlotte Deane, University of Oxford, UK
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Cristina Trujillo, Trinity College Dublin, Ireland
10 José Rafael Bordin, Universidade Federal de Pelotas, Brazil
11 Bruno A. C. Horta, Universidade Federal do Rio de Janeiro, Brazil
12 Tomás Pérez-Acle, Fundacion Ciencia & Vida, Centro Interdisciplinario de Neurociencia de
13 Valparaíso. Chile
14 Lu Zhang, Fujian Institute of Research on the Structure of Matter, Chinese Academy of
15 Sciences, China
16 Sergio Pantano, Institut Pasteur de Montevideo
17 E. Laura Coitiño, Facultad de Ciencias & CeInBio, Universidad de la República, Uruguay
18 Margot Paulino, Facultad de Química, Universidad de la República, Uruguay
19 Diniz Maciel de Sena Junior, Universidade Regional do Cariri, Brazil
20 Pilar Cossio, Biophysics of tropical diseases, Max Planck Tandem Group, University of
21 Antioquia, Colombia
22 Lee-Ping Wang, University of California at Davis, USA
23 Gaurav Chopra, Purdue University, USA
24 Wei Yang, Florida State University, USA
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Monica Pickholz, IFIBA, Universidad de Buenos Aires
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Esteban Vöhringer-Martinez, Universidad de Concepción, Chile
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Ram Samudrala, University at Buffalo, USA
29 Tiff Walsh, Deakin University, Australia
30 Zackary Falls, University at Buffalo, USA
31 Eliana Asciutto, ICIFI, UNSAM, Argentina
32 Alfredo Quevedo, Universidad Nacional de Córdoba, Argentina
33 T. Daniel Crawford, MolSSI Director / Virginia Tech, USA
34 Bettina G. Keller, Freie Universität Berlin, Germany
35 Horacio V. Guzman, Jozef Stefan Institute, Slovenia
36 Petra Imhof, Friedrich-Alexander Universität Erlangen-Nürnberg, Germany
37 Adolfo B. Poma, Institute of Fundamental Technological Research Polish Academy of Sciences,
38 Poland
39 Ignacio J. General, Universidad Nacional de San Martin & CONICET, Argentina
40 Sophia Yaliraki, Imperial College London, UK
41 Roberto D. Lins, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Brazil
42 Thomas L. Beck, Department of Chemistry, University of Cincinnati
43 Valerie Welborn, Department of Chemistry, Virginia Tech, USA
44 Julianna Oláh, Department of Inorganic and Analytical Chemistry, Budapest University, of
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Technology and Economics, Hungary
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Lipi Thukral, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
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Matthias Buck, Dept. of Physiology and Biophysics, Case Western Reserve University, USA
49 Franca Fraternali, Randall Centre for Cell and Molecular Biophysics, King’s College London, UK
50 Davide Marenduzzo, School of Physics and Astronomy, The University of Edinburgh, UK
51 Jeremy Smith, Oak Ridge National Lab, USA
52 Peter Tieleman, University of Calgary, Canada
53 Sergei Noskov, University of Calgary, Canada
54 Habibah A Wahab, Universiti Sains Malaysia, Malaysia
55 Rigoberto Hernandez, Department of Chemistry, Johns Hopkins University, USA
56 Pornpan Pungpo, Ubon Ratchathani University, Thailand
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3 Gregory R. Bowman, Washington University School of Medicine, USA
4 Renxiao Wang, Fudan University, China
5 Niu Huang, National Institute of Biological Sciences, Beijing, China
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Ekaterina Pas (née Izgorodina), Monash University, Australia
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Dusanka Janezic, University of Primorska, Slovenia
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F. Danilo Gonzalez-Nilo, CBIB Universidad Andres Bello, Santiago, Chile
10 Miguel Angel Mendez, Universidad San Francisco de Quito, Quito, Ecuador
11 Donald Hamelberg, Georgia State University, USA
12 Chung F. Wong, University of Missouri-St. Louis, USA
13 Lilian P. Davila, University of California Merced, USA
14 James Briggs, University of Houston, USA
15 Martin Zacharias, Technische Universität München, Germany
16 David Case, Rutgers University, USA
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