The need to implement FAIR principles in biomolecular simulations
Rommie Amaro
(1)
,
Johan Åqvist
(2)
,
Ivet Bahar
(3)
,
Federica Battistini
(4)
,
Adam Bellaiche
(5)
,
Daniel Beltran
(4)
,
Philip C. Biggin
(6)
,
Massimiliano Bonomi
(7)
,
Gregory R. Bowman
(8)
,
Richard Bryce
(9)
,
Giovanni Bussi
(10, 11)
,
Paolo Carloni
(12, 11)
,
David Case
(13)
,
Andrea Cavalli
(14, 15)
,
Chie-En A. Chang
(16)
,
Thomas E. Cheatham Iii
(17)
,
Margaret S. Cheung
(18, 19, 20)
,
Cris Chipot
(21, 22, 20)
,
Lillian T. Chong
(23)
,
Preeti Choudhary
(5)
,
Cecilia Clementi
(24)
,
Rosana Collepardo-Guevara
(25)
,
Peter Coveney
(26, 27)
,
T. Daniel Crawford
(28, 29)
,
Matteo Dal Peraro
(30)
,
Bert de Groot
(31)
,
Marina Guenza
(32)
,
Horacio V. Guzman
(33)
,
Lucie Delemotte
(34)
,
Marco de Vivo
(14)
,
Jonathan Essex
(35)
,
Franca Fraternali
(26)
,
Jiali Gao
(36)
,
Josep Lluís Gelpí
(37, 38)
,
Francesco Luigi Gervasio
(39, 26, 40)
,
Fernando Danilo Gonzalez-Nilo
(41)
,
Helmut Grubmüller
(31)
,
Sarah Harris
(42)
,
Teresa Head-Gordon
(43)
,
Rigoberto Hernandez
(44)
,
Adam Hospital
(4, 45)
,
Niu Huang
(46)
,
Xuhui Huang
(47)
,
Gerhard Hummer
(48, 49)
,
Javier Iglesias-Fernández
(50)
,
Jan H. Jensen
(51)
,
Shantenu Jha
(13)
,
Wanting Jiao
(52)
,
Shina Caroline Lynn Kamerlin
(2, 53)
,
Syma Khalid
(6)
,
Charles Laughton
(54)
,
Michael Levitt
(55)
,
Vittorio Limongelli
(56)
,
Erik Lindahl
(57, 34)
,
Kersten Lindorff-Larsen
(51)
,
Sharon Loverde
(58)
,
Magnus Lundborg
(34)
,
Yun Lina Luo
(59)
,
Francisco Javier Luque
(38)
,
Charlotte I. Lynch
(6)
,
Alexander Mackerell
(60)
,
Alessandra Magistrato
(10)
,
Siewert J. Marrink
(61)
,
Hugh Martin
(26)
,
J. Andrew Mccammon
(1)
,
Kenneth Merz
(62, 63)
,
Vicent Moliner
(64)
,
Adrian Mulholland
(65)
,
Sohail Murad
(66)
,
Athi N. Naganathan
(67)
,
Shikha Nangia
(68)
,
Frank Noe
(24, 69, 70)
,
Agnes Noy
(71)
,
Julianna Oláh
(72)
,
Megan O'Mara
(73)
,
Mary Jo Ondrechen
(74)
,
José N. Onuchic
(69)
,
Alexey Onufriev
(75)
,
Silvia Osuna
(76, 77)
,
Anna R. Panchenko
(78)
,
Sergio Pantano
(79)
,
Michele Parrinello
(14)
,
Alberto Perez
(80)
,
Tomas Perez-Acle
(81, 82)
,
Juan R. Perilla
(83, 22)
,
B. Montgomery Pettitt
(84)
,
Adriana Pietropalo
(85)
,
Jean-Philip Piquemal
(86)
,
Adolfo Poma
(87)
,
Matej Praprotnik
(88, 89)
,
Maria J. Ramos
(90)
,
Pengyu Ren
(91)
,
Nathalie Reuter
(92)
,
Adrian Roitberg
(80)
,
Edina Rosta
(26)
,
Carme Rovira
(38, 77)
,
Benoit Roux
(20)
,
Ursula Röthlisberger
(30)
,
Karissa Y. Sanbonmatsu
(93, 94)
,
Tamar Schlick
(95)
,
Alexey K. Shaytan
(96)
,
Carlos Simmerling
(3)
,
Jeremy C. Smith
(97, 98)
,
Yuji Sugita
(99, 100, 101)
,
Katarzyna Świderek
(64)
,
Makoto Taiji
(101)
,
Peng Tao
(102)
,
Julian Tirado-Rives
(103)
,
Inaki Tunón
(104)
,
Marc W. van der Kamp
(65)
,
David van der Spoel
(2)
,
Sameer Velankar
(5)
,
Gregory A. Voth
(20)
,
Rebecca Wade
(105)
,
Ariel Warshel
(106)
,
Valerie Vaissier Welborn
(29)
,
Stacey Wetmore
(107)
,
Chung F. Wong
(108)
,
Lee-Wei Yang
(109)
,
Martin Zacharias
(110)
,
Modesto Orozco
(4, 38)
1
UC San Diego -
University of California [San Diego]
2 Uppsala University
3 SBU - Stony Brook University [SUNY]
4 IRB - Institute for Research in Biomedicine [Barcelona, Spain]
5 EMBL-EBI - European Bioinformatics Institute [Hinxton]
6 University of Oxford
7 Département de Biologie structurale et Chimie - Department of Structural Biology and Chemistry
8 University of Pennsylvania
9 University of Manchester [Manchester]
10 SISSA / ISAS - Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies
11 UKA - Universitätsklinikum RWTH Aachen - University Hospital Aachen [Aachen, Germany]
12 FZJ - Forschungszentrum Jülich GmbH | Centre de recherche de Jülich | Jülich Research Centre
13 Rutgers - Rutgers University System
14 IIT - Italian Institute of Technology = Istituto Italiano di Tecnologia
15 CECAM - Centre Européen de Calcul Atomique et Moléculaire
16 UC Riverside - University of California [Riverside]
17 University of Utah
18 University of Washington [Seattle]
19 PNNL - Pacific Northwest National Laboratory
20 University of Chicago
21 LPCT - Laboratoire de Physique et Chimie Théoriques
22 UIUC - University of Illinois at Urbana-Champaign [Urbana]
23 PITT - University of Pittsburgh
24 Freie Universität Berlin
25 CAM - University of Cambridge [UK]
26 UCL - University College of London [London]
27 UvA - University of Amsterdam [Amsterdam] = Universiteit van Amsterdam
28 MolSSI - Molecular Sciences Software Institute [Blacksburg, USA]
29 Virginia Tech [Blacksburg]
30 EPFL - Ecole Polytechnique Fédérale de Lausanne
31 Max Planck Institute for Multidisciplinary Sciences / Max-Planck-Institut für Multidisziplinäre Naturwissenschaften [Göttingen, Germany]
32 University of Oregon [Eugene]
33 UAM - Universidad Autónoma de Madrid
34 KTH - KTH Royal Institute of Technology [Stockholm]
35 University of Southampton
36 UMN - University of Minnesota [Twin Cities]
37 BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
38 UB - Universitat de Barcelona
39 UNIGE - Université de Genève = University of Geneva
40 SIB - Swiss Institute of Bioinformatics [Genève]
41 UNAB - Universidad Andrés Bello [Santiago]
42 University of Sheffield [Sheffield]
43 UC Berkeley - University of California [Berkeley]
44 JHU - Johns Hopkins University
45 INB-ISCIII - Instituto Nacional de Bioinformática = Spanish National Bioinformatics Institute [Barcelona, Spain]
46 NIBS - National Institute of Biological Sciences [Beijing, China]
47 University of Wisconsin-Madison
48 MPIBP - Max-Planck-Institut für Biophysik - Max Planck Institute of Biophysics [Frankfurt am Main, Germany]
49 Goethe University Frankfurt
50 NBD - Nostrum Biodiscovery [Barcelona, Spain]
51 UCPH - University of Copenhagen = Københavns Universitet
52 Victoria University of Wellington
53 Georgia Institute of Technology [Atlanta]
54 UON - University of Nottingham, UK
55 Stanford University
56 USI - Università della Svizzera italiana = University of Italian Switzerland
57 Stockholm University
58 CUNY - City University of New York [New York]
59 Western University of Health Sciences
60 University of Maryland [Baltimore]
61 University of Groningen [Groningen]
62 Lerner Research Institute [Cleveland, OH, USA]
63 Michigan State University System
64 Universitat Jaume I = Jaume I University
65 University of Bristol [Bristol]
66 IIT - Illinois Institute of Technology
67 IIT Madras - Indian Institute of Technology Madras
68 Syracuse University
69 Rice University [Houston]
70 MSR AI4Sciences - Microsoft Research AI4Science [Berlin,Germany]
71 University of York [York, UK]
72 BME - Budapest University of Technology and Economics [Budapest]
73 UQ [All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations] - The University of Queensland
74 Northeastern University [Boston]
75 Virginia Polytechnic Institute and State University [Blacksburg]
76 UdG - Universitat de Girona = University of Girona
77 ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies
78 Queen's University [Kingston, Canada]
79 Institut Pasteur de Montevideo
80 UF - University of Florida [Gainesville]
81 Fundación Ciencia & Vida
82 USS - Universidad San Sebastian = San Sebastian University [Santiago, Chile]
83 University of Delaware [Newark]
84 UTMB - The University of Texas Medical Branch
85 UMG - Università degli Studi "Magna Graecia" di Catanzaro = University of Catanzaro
86 LCT - Laboratoire de chimie théorique
87 PAN - Polska Akademia Nauk = Polish Academy of Sciences = Académie polonaise des sciences
88 KI - National Institute of Chemistry [Llubljana]
89 University of Ljubljana
90 Universidade do Porto = University of Porto
91 University of Texas at Austin [Austin]
92 UiB - University of Bergen
93 LANL - Los Alamos National Laboratory
94 NMC - New Mexico Consortium
95 NYU - New York University [New York]
96 MSU - Lomonosov Moscow State University = Université d'État Lomonossov de Moscou [Moscou]
97 ORNL - Oak Ridge National Laboratory [Oak Ridge]
98 The University of Tennessee [Knoxville]
99 RIKEN CCS - RIKEN Center for Computational Science [Kobe]
100 RIKEN CPR - RIKEN Cluster for Pioneering Research (CPS)
101 RIKEN BDR - RIKEN Center for Biosystems Dynamics Research [Kobe]
102 SMU - Southern Methodist University [Dallas, TX, USA]
103 Yale University [New Haven]
104 UV - Universitat de València = University of Valencia
105 HITS - Heidelberg Institute for Theoretical Studies
106 USC - University of Southern California
107 University of Lethbridge
108 University of Missouri [St. Louis]
109 NTHU - National Tsing Hua University [Hsinchu]
110 TUM - Technische Universität Munchen - Technical University Munich - Université Technique de Munich
2 Uppsala University
3 SBU - Stony Brook University [SUNY]
4 IRB - Institute for Research in Biomedicine [Barcelona, Spain]
5 EMBL-EBI - European Bioinformatics Institute [Hinxton]
6 University of Oxford
7 Département de Biologie structurale et Chimie - Department of Structural Biology and Chemistry
8 University of Pennsylvania
9 University of Manchester [Manchester]
10 SISSA / ISAS - Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies
11 UKA - Universitätsklinikum RWTH Aachen - University Hospital Aachen [Aachen, Germany]
12 FZJ - Forschungszentrum Jülich GmbH | Centre de recherche de Jülich | Jülich Research Centre
13 Rutgers - Rutgers University System
14 IIT - Italian Institute of Technology = Istituto Italiano di Tecnologia
15 CECAM - Centre Européen de Calcul Atomique et Moléculaire
16 UC Riverside - University of California [Riverside]
17 University of Utah
18 University of Washington [Seattle]
19 PNNL - Pacific Northwest National Laboratory
20 University of Chicago
21 LPCT - Laboratoire de Physique et Chimie Théoriques
22 UIUC - University of Illinois at Urbana-Champaign [Urbana]
23 PITT - University of Pittsburgh
24 Freie Universität Berlin
25 CAM - University of Cambridge [UK]
26 UCL - University College of London [London]
27 UvA - University of Amsterdam [Amsterdam] = Universiteit van Amsterdam
28 MolSSI - Molecular Sciences Software Institute [Blacksburg, USA]
29 Virginia Tech [Blacksburg]
30 EPFL - Ecole Polytechnique Fédérale de Lausanne
31 Max Planck Institute for Multidisciplinary Sciences / Max-Planck-Institut für Multidisziplinäre Naturwissenschaften [Göttingen, Germany]
32 University of Oregon [Eugene]
33 UAM - Universidad Autónoma de Madrid
34 KTH - KTH Royal Institute of Technology [Stockholm]
35 University of Southampton
36 UMN - University of Minnesota [Twin Cities]
37 BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion
38 UB - Universitat de Barcelona
39 UNIGE - Université de Genève = University of Geneva
40 SIB - Swiss Institute of Bioinformatics [Genève]
41 UNAB - Universidad Andrés Bello [Santiago]
42 University of Sheffield [Sheffield]
43 UC Berkeley - University of California [Berkeley]
44 JHU - Johns Hopkins University
45 INB-ISCIII - Instituto Nacional de Bioinformática = Spanish National Bioinformatics Institute [Barcelona, Spain]
46 NIBS - National Institute of Biological Sciences [Beijing, China]
47 University of Wisconsin-Madison
48 MPIBP - Max-Planck-Institut für Biophysik - Max Planck Institute of Biophysics [Frankfurt am Main, Germany]
49 Goethe University Frankfurt
50 NBD - Nostrum Biodiscovery [Barcelona, Spain]
51 UCPH - University of Copenhagen = Københavns Universitet
52 Victoria University of Wellington
53 Georgia Institute of Technology [Atlanta]
54 UON - University of Nottingham, UK
55 Stanford University
56 USI - Università della Svizzera italiana = University of Italian Switzerland
57 Stockholm University
58 CUNY - City University of New York [New York]
59 Western University of Health Sciences
60 University of Maryland [Baltimore]
61 University of Groningen [Groningen]
62 Lerner Research Institute [Cleveland, OH, USA]
63 Michigan State University System
64 Universitat Jaume I = Jaume I University
65 University of Bristol [Bristol]
66 IIT - Illinois Institute of Technology
67 IIT Madras - Indian Institute of Technology Madras
68 Syracuse University
69 Rice University [Houston]
70 MSR AI4Sciences - Microsoft Research AI4Science [Berlin,Germany]
71 University of York [York, UK]
72 BME - Budapest University of Technology and Economics [Budapest]
73 UQ [All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations] - The University of Queensland
74 Northeastern University [Boston]
75 Virginia Polytechnic Institute and State University [Blacksburg]
76 UdG - Universitat de Girona = University of Girona
77 ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies
78 Queen's University [Kingston, Canada]
79 Institut Pasteur de Montevideo
80 UF - University of Florida [Gainesville]
81 Fundación Ciencia & Vida
82 USS - Universidad San Sebastian = San Sebastian University [Santiago, Chile]
83 University of Delaware [Newark]
84 UTMB - The University of Texas Medical Branch
85 UMG - Università degli Studi "Magna Graecia" di Catanzaro = University of Catanzaro
86 LCT - Laboratoire de chimie théorique
87 PAN - Polska Akademia Nauk = Polish Academy of Sciences = Académie polonaise des sciences
88 KI - National Institute of Chemistry [Llubljana]
89 University of Ljubljana
90 Universidade do Porto = University of Porto
91 University of Texas at Austin [Austin]
92 UiB - University of Bergen
93 LANL - Los Alamos National Laboratory
94 NMC - New Mexico Consortium
95 NYU - New York University [New York]
96 MSU - Lomonosov Moscow State University = Université d'État Lomonossov de Moscou [Moscou]
97 ORNL - Oak Ridge National Laboratory [Oak Ridge]
98 The University of Tennessee [Knoxville]
99 RIKEN CCS - RIKEN Center for Computational Science [Kobe]
100 RIKEN CPR - RIKEN Cluster for Pioneering Research (CPS)
101 RIKEN BDR - RIKEN Center for Biosystems Dynamics Research [Kobe]
102 SMU - Southern Methodist University [Dallas, TX, USA]
103 Yale University [New Haven]
104 UV - Universitat de València = University of Valencia
105 HITS - Heidelberg Institute for Theoretical Studies
106 USC - University of Southern California
107 University of Lethbridge
108 University of Missouri [St. Louis]
109 NTHU - National Tsing Hua University [Hsinchu]
110 TUM - Technische Universität Munchen - Technical University Munich - Université Technique de Munich
Massimiliano Bonomi
- Fonction : Auteur
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- IdHAL : massimiliano-bonomi
- ORCID : 0000-0002-7321-0004
- IdRef : 237807793
Jean-Philip Piquemal
- Fonction : Auteur
- PersonId : 7807
- IdHAL : jean-philip-piquemal
- ORCID : 0000-0001-6615-9426
- IdRef : 089289439
Résumé
This letter illustrates the opinion of the molecular dynamics (MD) community on the need to adopt a new FAIR paradigm for the use of molecular simulations. It highlights the necessity of a collaborative effort to create, establish, and sustain a database that allows findability, accessibility, interoperability, and reusability of molecular dynamics simulation data. Such a development would democratize the field and significantly improve the impact of MD simulations on life science research. This will transform our working paradigm, pushing the field to a new frontier. We invite you to support our initiative at the MDDB community (https://mddbr.eu/community/)
