The need to implement FAIR principles in biomolecular simulations
Abstract
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
Cite
@article{arxiv.2407.16584,
title = {The need to implement FAIR principles in biomolecular simulations},
author = {Rommie Amaro and Johan Åqvist and Ivet Bahar and Federica Battistini and Adam Bellaiche and Daniel Beltran and Philip C. Biggin and Massimiliano Bonomi and Gregory R. Bowman and Richard Bryce and Giovanni Bussi and Paolo Carloni and David Case and Andrea Cavalli and Chie-En A. Chang and Thomas E. Cheatham and Margaret S. Cheung and Cris Chipot and Lillian T. Chong and Preeti Choudhary and Gerardo Andres Cisneros and Cecilia Clementi and Rosana Collepardo-Guevara and Peter Coveney and Roberto Covino and T. Daniel Crawford and Matteo Dal Peraro and Bert de Groot and Lucie Delemotte and Marco De Vivo and Jonathan Essex and Franca Fraternali and Jiali Gao and Josep Lluís Gelpí and Francesco Luigi Gervasio and Fernando Danilo Gonzalez-Nilo and Helmut Grubmüller and Marina Guenza and Horacio V. Guzman and Sarah Harris and Teresa Head-Gordon and Rigoberto Hernandez and Adam Hospital and Niu Huang and Xuhui Huang and Gerhard Hummer and Javier Iglesias-Fernández and Jan H. Jensen and Shantenu Jha and Wanting Jiao and William L. Jorgensen and Shina Caroline Lynn Kamerlin and Syma Khalid and Charles Laughton and Michael Levitt and Vittorio Limongelli and Erik Lindahl and Kresten Lindorff-Larsen and Sharon Loverde and Magnus Lundborg and Yun Lyna Luo and Francisco Javier Luque and Charlotte I. Lynch and Alexander MacKerell and Alessandra Magistrato and Siewert J. Marrink and Hugh Martin and J. Andrew McCammon and Kenneth Merz and Vicent Moliner and Adrian Mulholland and Sohail Murad and Athi N. Naganathan and Shikha Nangia and Frank Noe and Agnes Noy and Julianna Oláh and Megan O'Mara and Mary Jo Ondrechen and José N. Onuchic and Alexey Onufriev and Silvia Osuna and Anna R. Panchenko and Sergio Pantano and Carol Parish and Michele Parrinello and Alberto Perez and Tomas Perez-Acle and Juan R. Perilla and B. Montgomery Pettitt and Adriana Pietropalo and Jean-Philip Piquemal and Adolfo Poma and Matej Praprotnik and Maria J. Ramos and Pengyu Ren and Nathalie Reuter and Adrian Roitberg and Edina Rosta and Carme Rovira and Benoit Roux and Ursula Röthlisberger and Karissa Y. Sanbonmatsu and Tamar Schlick and Alexey K. Shaytan and Carlos Simmerling and Jeremy C. Smith and Yuji Sugita and Katarzyna Świderek and Makoto Taiji and Peng Tao and D. Peter Tieleman and Irina G. Tikhonova and Julian Tirado-Rives and Inaki Tunón and Marc W. Van Der Kamp and David Van der Spoel and Sameer Velankar and Gregory A. Voth and Rebecca Wade and Ariel Warshel and Valerie Vaissier Welborn and Stacey Wetmore and Travis J. Wheeler and Chung F. Wong and Lee-Wei Yang and Martin Zacharias and Modesto Orozco},
journal= {arXiv preprint arXiv:2407.16584},
year = {2025}
}