Article Dans Une Revue Nature Methods Année : 2025

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 Biggin , Massimiliano Bonomi (6) , Gregory Bowman , Richard Bryce (7) , Giovanni Bussi (8, 9) , Paolo Carloni (10, 9) , David Case (11) , Andrea Cavalli (12, 13) , Chia-En Chang , Thomas Cheatham , Margaret Cheung , Christophe Chipot , Lillian Chong , Preeti Choudhary (5) , G. Andres Cisneros , Cecilia Clementi (14) , Rosana Collepardo-Guevara (15) , Peter Coveney (16, 17) , Roberto Covino , T. Daniel Crawford (18, 19) , Matteo Dal Peraro , Bert de Groot (20) , Lucie Delemotte (21) , Marco de Vivo (12) , Jonathan Essex (22) , Franca Fraternali (16) , Jiali Gao (23) , Josep Ll. Gelpí , Francesco Gervasio , Fernando González-Nilo , Helmut Grubmüller (20) , Marina Guenza (24) , Horacio Guzman , Sarah Harris (25) , Teresa Head-Gordon (26) , Rigoberto Hernandez (27) , Adam Hospital (4, 28) , Niu Huang (29) , Xuhui Huang (30) , Gerhard Hummer (31, 32) , Javier Iglesias-Fernández (33) , Jan Jensen , Shantenu Jha (11) , Wanting Jiao (34) , William Jorgensen , Shina Kamerlin , Syma Khalid (35) , Charles Laughton (36) , Michael Levitt (37) , Vittorio Limongelli (38) , Erik Lindahl (39, 21) , Kresten Lindorff-Larsen , Sharon Loverde (40) , Magnus Lundborg (21) , Yun Luo , F. Javier Luque , Charlotte Lynch , Alexander Mackerell (41) , Alessandra Magistrato (8) , Siewert Marrink , Hugh Martin (16) , J. Andrew Mccammon (1) , Kenneth Merz (42, 43) , Vicent Moliner (44) , Adrian Mulholland (45) , Sohail Murad (46) , Athi Naganathan , Shikha Nangia (47) , Frank Noe (14, 48, 49) , Agnes Noy (50) , Julianna Oláh (51) , Megan O’mara , Mary Jo Ondrechen (52) , Jose Onuchic , Alexey Onufriev (53) , Sílvia Osuna (54, 55) , Giulia Palermo , Anna Panchenko , Sergio Pantano (56) , Carol Parish , Michele Parrinello (12) , Alberto Perez (57) , Tomas Perez-Acle (58, 59) , Juan Perilla , B. Montgomery Pettitt (60) , Adriana Pietropaolo , Jean-Philip Piquemal (61) , Adolfo Poma (62) , Matej Praprotnik (63, 64) , Maria Ramos , Pengyu Ren (65) , Nathalie Reuter (66) , Adrian Roitberg (57) , Edina Rosta (16) , Carme Rovira (67, 55) , Benoit Roux (68) , Ursula Röthlisberger (69) , Karissa Sanbonmatsu , Tamar Schlick (70) , Alexey Shaytan , Carlos Simmerling (3) , Jeremy Smith , Yuji Sugita (71, 72, 73) , Katarzyna Świderek (44) , Makoto Taiji (73) , Peng Tao (74) , D. Peter Tieleman , Irina Tikhonova , Julian Tirado-Rives (75) , Iñaki Tuñón (76) , Marc van der Kamp , David van der Spoel (2) , Sameer Velankar (5) , Gregory Voth , Rebecca Wade (77) , Ariel Warshel (78) , Valerie Vaissier Welborn (19) , Stacey Wetmore (79) , Travis Wheeler , Chung Wong , Lee-Wei Yang (80) , Martin Zacharias (81) , Modesto Orozco (4, 67)
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 Département de Biologie structurale et Chimie - Department of Structural Biology and Chemistry
7 University of Manchester [Manchester]
8 SISSA / ISAS - Scuola Internazionale Superiore di Studi Avanzati = International School for Advanced Studies [Trieste]
9 UKA - Universitätsklinikum RWTH Aachen - University Hospital Aachen [Aachen, Germany]
10 FZJ - Forschungszentrum Jülich GmbH | Centre de recherche de Jülich | Juelich Research Centre
11 Rutgers - Rutgers University System
12 IIT - Italian Institute of Technology = Istituto Italiano di Tecnologia [Genova]
13 CECAM - Centre Européen de Calcul Atomique et Moléculaire
14 Freie Universität Berlin = Free University of Berlin
15 CAM - University of Cambridge [Cambridge, UK]
16 UCL - University College London [UCL]
17 UvA - Universiteit van Amsterdam = University of Amsterdam
18 MolSSI - Molecular Sciences Software Institute [Blacksburg, USA]
19 Virginia Tech [Blacksburg]
20 Max Planck Institute for Multidisciplinary Sciences / Max-Planck-Institut für Multidisziplinäre Naturwissenschaften [Göttingen, Germany]
21 KTH - KTH Royal Institute of Technology [Stockholm]
22 University of Southampton
23 UMN - University of Minnesota [Twin Cities]
24 University of Oregon [Eugene]
25 University of Sheffield [Sheffield]
26 UC Berkeley - University of California [Berkeley]
27 JHU - Johns Hopkins University [Baltimore]
28 INB-ISCIII - Instituto Nacional de Bioinformática = Spanish National Bioinformatics Institute [Barcelona, Spain]
29 NIBS - National Institute of Biological Sciences [Beijing, China]
30 University of Wisconsin-Madison
31 MPIBP - Max-Planck-Institut für Biophysik - Max Planck Institute of Biophysics [Frankfurt am Main, Germany]
32 Goethe University Frankfurt = Goethe-Universität Frankfurt am Main
33 NBD - Nostrum Biodiscovery [Barcelona, Spain]
34 Victoria University of Wellington
35 University of Oxford
36 UON - University of Nottingham, UK
37 Stanford University
38 USI - Università della Svizzera italiana = University of Italian Switzerland
39 Stockholm University
40 CUNY - City University of New York [New York]
41 UMB - University of Maryland [Baltimore]
42 Lerner Research Institute [Cleveland, OH, USA]
43 Michigan State University System
44 Universitat Jaume I = Jaume I University
45 University of Bristol [Bristol]
46 IIT - Illinois Institute of Technology
47 Syracuse University
48 Rice University [Houston]
49 MSR AI4Sciences - Microsoft Research AI4Science [Berlin,Germany]
50 University of York [York, UK]
51 BME - Budapest University of Technology and Economics [Budapest]
52 Northeastern University [Boston]
53 Virginia Polytechnic Institute and State University [Blacksburg]
54 UdG - Universitat de Girona = University of Girona
55 ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies
56 Institut Pasteur de Montevideo
57 UF - University of Florida [Gainesville]
58 Fundación Ciencia & Vida
59 USS - Universidad San Sebastian = San Sebastian University [Santiago, Chile]
60 UTMB - The University of Texas Medical Branch
61 LCT - Laboratoire de chimie théorique
62 PAN - Polska Akademia Nauk = Polish Academy of Sciences = Académie polonaise des sciences
63 KI - National Institute of Chemistry [Ljubljana]
64 University of Ljubljana
65 University of Texas at Austin [Austin]
66 UiB - University of Bergen
67 UB - Universitat de Barcelona
68 University of Chicago
69 EPFL - Ecole Polytechnique Fédérale de Lausanne
70 NYU - New York University [New York]
71 RIKEN CCS - RIKEN Center for Computational Science [Kobe]
72 RIKEN PRI - RIKEN Cluster for Pioneering Research
73 RIKEN BDR - RIKEN Center for Biosystems Dynamics Research [Kobe]
74 SMU - Southern Methodist University [Dallas, TX, USA]
75 Yale University [New Haven]
76 UV - Universitat de València = University of Valencia = Universidade de Valencia
77 HITS - Heidelberg Institute for Theoretical Studies
78 USC - University of Southern California
79 University of Lethbridge
80 NTHU - National Tsing Hua University [Hsinchu]
81 TUM - Technische Universität Munchen = Technical University Munich = Université Technique de Munich
Ivet Bahar
Philip Biggin
  • Fonction : Auteur
Gregory Bowman
Chia-En Chang
  • Fonction : Auteur
Thomas Cheatham
  • Fonction : Auteur
Margaret Cheung
  • Fonction : Auteur
Christophe Chipot
Lillian Chong
  • Fonction : Auteur
G. Andres Cisneros
Roberto Covino
Matteo Dal Peraro
Jonathan Essex
Josep Ll. Gelpí
Francesco Gervasio
Fernando González-Nilo
Marina Guenza
Horacio Guzman
Xuhui Huang
Jan Jensen
  • Fonction : Auteur
Wanting Jiao
William Jorgensen
  • Fonction : Auteur
Shina Kamerlin
Syma Khalid
Charles Laughton
Kresten Lindorff-Larsen
Yun Luo
F. Javier Luque
Charlotte Lynch
Siewert Marrink
Adrian Mulholland
Athi Naganathan
Agnes Noy
Megan O’mara
Mary Jo Ondrechen
Jose Onuchic
Giulia Palermo
  • Fonction : Auteur
Anna Panchenko
  • Fonction : Auteur
Carol Parish
  • Fonction : Auteur
Juan Perilla
Adriana Pietropaolo
  • Fonction : Auteur
Maria Ramos
  • Fonction : Auteur
Nathalie Reuter
Benoit Roux
Karissa Sanbonmatsu
Alexey Shaytan
  • Fonction : Auteur
Carlos Simmerling
Jeremy Smith
D. Peter Tieleman
Irina Tikhonova
Julian Tirado-Rives
Marc van der Kamp
  • Fonction : Auteur
David van der Spoel
Gregory Voth
  • Fonction : Auteur
Ariel Warshel
Stacey Wetmore
Travis Wheeler
  • Fonction : Auteur
Chung Wong
  • Fonction : Auteur

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/)

Dates et versions

hal-04663318 , version 1 (27-07-2024)

Identifiants

Citer

Rommie Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, et al.. The need to implement FAIR principles in biomolecular simulations. Nature Methods, 2025, ⟨10.1038/s41592-025-02635-0⟩. ⟨hal-04663318⟩
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