The need to implement FAIR principles in biomolecular simulations

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

doi:10.1038/s41592-025-02635-0

In the Big Data era, a change of paradigm in the use of molecular dynamics is required. Trajectories should be stored under FAIR (findable, accessible, interoperable and reusable) requirements to favor its reuse by the community under an open science paradigm

The need to implement FAIR principles in biomolecular simulations / Amaro, Rommie E.; Åqvist, Johan; Bahar, Ivet; Battistini, Federica; Bellaiche, Adam; Beltran, Daniel; Biggin, Philip C.; Bonomi, Massimiliano; Bowman, Gregory R.; Bryce, Richard A.; Bussi, Giovanni; Carloni, Paolo; Case, David A.; Cavalli, Andrea; Chang, Chia-En A.; Cheatham, Thomas E.; Cheung, Margaret S.; Chipot, Christophe; Chong, Lillian T.; Choudhary, Preeti; Cisneros, G. Andres; Clementi, Cecilia; Collepardo-Guevara, Rosana; Coveney, Peter; Covino, Roberto; Crawford, T. Daniel; Dal Peraro, Matteo; de Groot, Bert L.; Delemotte, Lucie; De Vivo, Marco; Essex, Jonathan W.; Fraternali, Franca; Gao, Jiali; Gelpí, Josep Ll.; Gervasio, Francesco L.; González-Nilo, Fernando D.; Grubmüller, Helmut; Guenza, Marina G.; Guzman, Horacio V.; Harris, Sarah; Head-Gordon, Teresa; Hernandez, Rigoberto; Hospital, Adam; Huang, Niu; Huang, Xuhui; Hummer, Gerhard; Iglesias-Fernández, Javier; Jensen, Jan H.; Jha, Shantenu; Jiao, Wanting; Jorgensen, William L.; Kamerlin, Shina C. L.; Khalid, Syma; Laughton, Charles; Levitt, Michael; Limongelli, Vittorio; Lindahl, Erik; Lindorff-Larsen, Kresten; Loverde, Sharon; Lundborg, Magnus; Luo, Yun L.; Luque, F. Javier; Lynch, Charlotte I.; Mackerell, Alexander D.; Magistrato, Alessandra; Marrink, Siewert J.; Martin, Hugh; Mccammon, J. Andrew; Merz, Kenneth; Moliner, Vicent; Mulholland, Adrian J.; Murad, Sohail; Naganathan, Athi N.; Nangia, Shikha; Noe, Frank; Noy, Agnes; Oláh, Julianna; O'Mara, Megan L.; Ondrechen, Mary Jo; Onuchic, Jose N.; Onufriev, Alexey; Osuna, Sílvia; Palermo, Giulia; Panchenko, Anna R.; Pantano, Sergio; Parish, Carol; Parrinello, Michele; Perez, Alberto; Perez-Acle, Tomas; Perilla, Juan R.; Pettitt, B. Montgomery; Pietropaolo, Adriana; Piquemal, Jean-Philip; Poma, Adolfo B.; Praprotnik, Matej; Ramos, Maria J.; Ren, Pengyu; Reuter, Nathalie; Roitberg, Adrian; Rosta, Edina; Rovira, Carme; Roux, Benoit; Rothlisberger, Ursula; Sanbonmatsu, Karissa Y.; Schlick, Tamar; Shaytan, Alexey K.; Simmerling, Carlos; Smith, Jeremy C.; Sugita, Yuji; Świderek, Katarzyna; Taiji, Makoto; Tao, Peng; Tieleman, D. Peter; Tikhonova, Irina G.; Tirado-Rives, Julian; Tuñón, Iñaki; van der Kamp, Marc W.; van der Spoel, David; Velankar, Sameer; Voth, Gregory A.; Wade, Rebecca; Warshel, Ariel; Welborn, Valerie Vaissier; Wetmore, Stacey D.; Wheeler, Travis J.; Wong, Chung F.; Yang, Lee-Wei; Zacharias, Martin; Orozco, Modesto. - In: NATURE METHODS. - ISSN 1548-7091. - 22:(2025), pp. 641-645. [10.1038/s41592-025-02635-0]