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arxiv: 2407.16584 · v4 · pith:SLZEPNGG · submitted 2024-07-23 · q-bio.BM

The need to implement FAIR principles in biomolecular simulations

Rommie Amaro , Johan {\AA}qvist , Ivet Bahar , Federica Battistini , Adam Bellaiche , Daniel Beltran , Philip C. Biggin , Massimiliano Bonomi
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Gregory R. Bowman Richard Bryce Giovanni Bussi Paolo Carloni David Case Andrea Cavalli Chie-En A. Chang Thomas E. Cheatham III Margaret S. Cheung Cris Chipot Lillian T. Chong Preeti Choudhary Gerardo Andres Cisneros Cecilia Clementi Rosana Collepardo-Guevara Peter Coveney Roberto Covino T. Daniel Crawford Matteo Dal Peraro Bert de Groot Lucie Delemotte Marco De Vivo Jonathan Essex Franca Fraternali Jiali Gao Josep Llu\'is Gelp\'i Francesco Luigi Gervasio Fernando Danilo Gonzalez-Nilo Helmut Grubm\"uller Marina Guenza Horacio V. Guzman Sarah Harris Teresa Head-Gordon Rigoberto Hernandez Adam Hospital Niu Huang Xuhui Huang Gerhard Hummer Javier Iglesias-Fern\'andez Jan H. Jensen Shantenu Jha Wanting Jiao William L. Jorgensen Shina Caroline Lynn Kamerlin Syma Khalid Charles Laughton Michael Levitt Vittorio Limongelli Erik Lindahl Kresten Lindorff-Larsen Sharon Loverde Magnus Lundborg Yun Lyna Luo Francisco Javier Luque Charlotte I. Lynch Alexander MacKerell Alessandra Magistrato Siewert J. Marrink Hugh Martin J. Andrew McCammon Kenneth Merz Vicent Moliner Adrian Mulholland Sohail Murad Athi N. Naganathan Shikha Nangia Frank Noe Agnes Noy Julianna Ol\'ah Megan O'Mara Mary Jo Ondrechen Jos\'e N. Onuchic Alexey Onufriev Silvia Osuna Anna R. Panchenko Sergio Pantano Carol Parish Michele Parrinello Alberto Perez Tomas Perez-Acle Juan R. Perilla B. Montgomery Pettitt Adriana Pietropalo Jean-Philip Piquemal Adolfo Poma Matej Praprotnik Maria J. Ramos Pengyu Ren Nathalie Reuter Adrian Roitberg Edina Rosta Carme Rovira Benoit Roux Ursula R\"othlisberger Karissa Y. Sanbonmatsu Tamar Schlick Alexey K. Shaytan Carlos Simmerling Jeremy C. Smith Yuji Sugita Katarzyna \'Swiderek Makoto Taiji Peng Tao D. Peter Tieleman Irina G. Tikhonova Julian Tirado-Rives Inaki Tun\'on Marc W. Van Der Kamp David Van der Spoel Sameer Velankar Gregory A. Voth Rebecca Wade Ariel Warshel Valerie Vaissier Welborn Stacey Wetmore Travis J. Wheeler Chung F. Wong Lee-Wei Yang Martin Zacharias Modesto Orozco
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classification q-bio.BM
keywords simulationscommunityfairmolecularneedbiomoleculardynamicsfield
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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/) Now published as: Amaro, R.E., et al. The need to implement FAIR principles in biomolecular simulations. Nat Methods (2025) https://doi.org/10.1038/s41592-025-02635-0

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