The need to implement FAIR principles in biomolecular simulations

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

doi:10.1038/s41592-025-02635-0

The need to implement FAIR principles in biomolecular simulations

Rommie E. Amaro
, Johan Åqvist
, Ivet Bahar
, Federica Battistini
, Adam Bellaiche
, Daniel Beltran
, Philip C. Biggin
, Massimiliano Bonomi
, Gregory R. Bowman
, Richard A. Bryce
, Giovanni Bussi
, Paolo Carloni
, David A. Case
, Andrea Cavalli
, Chia En A. Chang
, Thomas E. Cheatham
, Margaret S. Cheung
, Christophe Chipot
, Lillian T. Chong
, Preeti Choudhary

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

Laufer Center for Physical and Quantitative Biology

Stony Brook University

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Research output: Contribution to journal › Comment/debate

35 Scopus citations

Abstract

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.

Original language	English
Article number	268
Pages (from-to)	641-645
Number of pages	5
Journal	Nature Methods
Volume	22
Issue number	4
DOIs	https://doi.org/10.1038/s41592-025-02635-0
State	Published - Apr 2025

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Cite this

Amaro, R. E., Åqvist, J., Bahar, I., Battistini, F., Bellaiche, A., Beltran, D., Biggin, P. C., Bonomi, M., Bowman, G. R., Bryce, R. A., Bussi, G., Carloni, P., Case, D. A., Cavalli, A., Chang, C. E. A., Cheatham, T. E., Cheung, M. S., Chipot, C., Chong, L. T., ... Orozco, M. (2025). The need to implement FAIR principles in biomolecular simulations. Nature Methods, 22(4), 641-645. Article 268. https://doi.org/10.1038/s41592-025-02635-0

@article{c08214ecc4e2413e8286093c5cc2ff6c,

title = "The need to implement FAIR principles in biomolecular simulations",

abstract = "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.",

author = "Amaro, \{Rommie E.\} and Johan {\AA}qvist and Ivet Bahar and Federica Battistini and Adam Bellaiche and Daniel Beltran and Biggin, \{Philip C.\} and Massimiliano Bonomi and Bowman, \{Gregory R.\} and Bryce, \{Richard A.\} and Giovanni Bussi and Paolo Carloni and Case, \{David A.\} and Andrea Cavalli and Chang, \{Chia En A.\} and Cheatham, \{Thomas E.\} and Cheung, \{Margaret S.\} and Christophe Chipot and Chong, \{Lillian T.\} and Preeti Choudhary and Cisneros, \{G. Andres\} and Cecilia Clementi and Rosana Collepardo-Guevara and Peter Coveney and Roberto Covino and Crawford, \{T. Daniel\} and \{Dal Peraro\}, Matteo and \{de Groot\}, \{Bert L.\} and Lucie Delemotte and \{De Vivo\}, Marco and Essex, \{Jonathan W.\} and Franca Fraternali and Jiali Gao and Gelp{\'i}, \{Josep Ll\} and Gervasio, \{Francesco L.\} and Gonz{\'a}lez-Nilo, \{Fernando D.\} and Helmut Grubm{\"u}ller and Guenza, \{Marina G.\} and Guzman, \{Horacio V.\} 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-Fern{\'a}ndez and Jensen, \{Jan H.\} and Shantenu Jha and Wanting Jiao and Jorgensen, \{William L.\} and Kamerlin, \{Shina C.L.\} 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 Luo, \{Yun L.\} and Luque, \{F. Javier\} and Lynch, \{Charlotte I.\} and MacKerell, \{Alexander D.\} and Alessandra Magistrato and Marrink, \{Siewert J.\} and Hugh Martin and McCammon, \{J. Andrew\} and Kenneth Merz and Vicent Moliner and Mulholland, \{Adrian J.\} and Sohail Murad and Naganathan, \{Athi N.\} and Shikha Nangia and Frank Noe and Agnes Noy and Julianna Ol{\'a}h and O{\textquoteright}Mara, \{Megan L.\} and Ondrechen, \{Mary Jo\} and Onuchic, \{Jose N.\} and Alexey Onufriev and S{\'i}lvia Osuna and Giulia Palermo and Panchenko, \{Anna R.\} and Sergio Pantano and Carol Parish and Michele Parrinello and Alberto Perez and Tomas Perez-Acle and Perilla, \{Juan R.\} and Pettitt, \{B. Montgomery\} and Adriana Pietropaolo and Piquemal, \{Jean Philip\} and Poma, \{Adolfo B.\} and Matej Praprotnik and Ramos, \{Maria J.\} and Pengyu Ren and Nathalie Reuter and Adrian Roitberg and Edina Rosta and Carme Rovira and Benoit Roux and Ursula Rothlisberger and Sanbonmatsu, \{Karissa Y.\} and Tamar Schlick and Shaytan, \{Alexey K.\} and Carlos Simmerling and Smith, \{Jeremy C.\} and Yuji Sugita and Katarzyna {\'S}widerek and Makoto Taiji and Peng Tao and Tieleman, \{D. Peter\} and Tikhonova, \{Irina G.\} and Julian Tirado-Rives and I{\~n}aki Tu{\~n}{\'o}n and \{van der Kamp\}, \{Marc W.\} and \{van der Spoel\}, David and Sameer Velankar and Voth, \{Gregory A.\} and Rebecca Wade and Ariel Warshel and Welborn, \{Valerie Vaissier\} and Wetmore, \{Stacey D.\} and Wheeler, \{Travis J.\} and Wong, \{Chung F.\} and Yang, \{Lee Wei\} and Martin Zacharias and Modesto Orozco",

note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive licence to Springer Nature America, Inc. 2025.",

year = "2025",

month = apr,

doi = "10.1038/s41592-025-02635-0",

language = "English",

volume = "22",

pages = "641--645",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

number = "4",

}

Amaro, RE, Åqvist, J, Bahar, I, Battistini, F, Bellaiche, A, Beltran, D, Biggin, PC, Bonomi, M, Bowman, GR, Bryce, RA, Bussi, G, Carloni, P, Case, DA, Cavalli, A, Chang, CEA, Cheatham, TE, Cheung, MS, Chipot, C, Chong, LT, Choudhary, P, Cisneros, GA, Clementi, C, Collepardo-Guevara, R, Coveney, P, Covino, R, Crawford, TD, Dal Peraro, M, de Groot, BL, Delemotte, L, De Vivo, M, Essex, JW, Fraternali, F, Gao, J, Gelpí, JL, Gervasio, FL, González-Nilo, FD, Grubmüller, H, Guenza, MG, Guzman, HV, Harris, S, Head-Gordon, T, Hernandez, R, Hospital, A, Huang, N, Huang, X, Hummer, G, Iglesias-Fernández, J, Jensen, JH, Jha, S, Jiao, W, Jorgensen, WL, Kamerlin, SCL, Khalid, S, Laughton, C, Levitt, M, Limongelli, V, Lindahl, E, Lindorff-Larsen, K, Loverde, S, Lundborg, M, Luo, YL, Luque, FJ, Lynch, CI, MacKerell, AD, Magistrato, A, Marrink, SJ, Martin, H, McCammon, JA, Merz, K, Moliner, V, Mulholland, AJ, Murad, S, Naganathan, AN, Nangia, S, Noe, F, Noy, A, Oláh, J, O’Mara, ML, Ondrechen, MJ, Onuchic, JN, Onufriev, A, Osuna, S, Palermo, G, Panchenko, AR, Pantano, S, Parish, C, Parrinello, M, Perez, A, Perez-Acle, T, Perilla, JR, Pettitt, BM, Pietropaolo, A, Piquemal, JP, Poma, AB, Praprotnik, M, Ramos, MJ, Ren, P, Reuter, N, Roitberg, A, Rosta, E, Rovira, C, Roux, B, Rothlisberger, U, Sanbonmatsu, KY, Schlick, T, Shaytan, AK, Simmerling, C, Smith, JC, Sugita, Y, Świderek, K, Taiji, M, Tao, P, Tieleman, DP, Tikhonova, IG, Tirado-Rives, J, Tuñón, I, van der Kamp, MW, van der Spoel, D, Velankar, S, Voth, GA, Wade, R, Warshel, A, Welborn, VV, Wetmore, SD, Wheeler, TJ, Wong, CF, Yang, LW, Zacharias, M & Orozco, M 2025, 'The need to implement FAIR principles in biomolecular simulations', Nature Methods, vol. 22, no. 4, 268, pp. 641-645. https://doi.org/10.1038/s41592-025-02635-0

TY - JOUR

T1 - The need to implement FAIR principles in biomolecular simulations

AU - Amaro, Rommie E.

AU - Åqvist, Johan

AU - Bahar, Ivet

AU - Battistini, Federica

AU - Bellaiche, Adam

AU - Beltran, Daniel

AU - Biggin, Philip C.

AU - Bonomi, Massimiliano

AU - Bowman, Gregory R.

AU - Bryce, Richard A.

AU - Bussi, Giovanni

AU - Carloni, Paolo

AU - Case, David A.

AU - Cavalli, Andrea

AU - Chang, Chia En A.

AU - Cheatham, Thomas E.

AU - Cheung, Margaret S.

AU - Chipot, Christophe

AU - Chong, Lillian T.

AU - Choudhary, Preeti

AU - Cisneros, G. Andres

AU - Clementi, Cecilia

AU - Collepardo-Guevara, Rosana

AU - Coveney, Peter

AU - Covino, Roberto

AU - Crawford, T. Daniel

AU - Dal Peraro, Matteo

AU - de Groot, Bert L.

AU - Delemotte, Lucie

AU - De Vivo, Marco

AU - Essex, Jonathan W.

AU - Fraternali, Franca

AU - Gao, Jiali

AU - Gelpí, Josep Ll

AU - Gervasio, Francesco L.

AU - González-Nilo, Fernando D.

AU - Grubmüller, Helmut

AU - Guenza, Marina G.

AU - Guzman, Horacio V.

AU - Harris, Sarah

AU - Head-Gordon, Teresa

AU - Hernandez, Rigoberto

AU - Hospital, Adam

AU - Huang, Niu

AU - Huang, Xuhui

AU - Hummer, Gerhard

AU - Iglesias-Fernández, Javier

AU - Jensen, Jan H.

AU - Jha, Shantenu

AU - Jiao, Wanting

AU - Jorgensen, William L.

AU - Kamerlin, Shina C.L.

AU - Khalid, Syma

AU - Laughton, Charles

AU - Levitt, Michael

AU - Limongelli, Vittorio

AU - Lindahl, Erik

AU - Lindorff-Larsen, Kresten

AU - Loverde, Sharon

AU - Lundborg, Magnus

AU - Luo, Yun L.

AU - Luque, F. Javier

AU - Lynch, Charlotte I.

AU - MacKerell, Alexander D.

AU - Magistrato, Alessandra

AU - Marrink, Siewert J.

AU - Martin, Hugh

AU - McCammon, J. Andrew

AU - Merz, Kenneth

AU - Moliner, Vicent

AU - Mulholland, Adrian J.

AU - Murad, Sohail

AU - Naganathan, Athi N.

AU - Nangia, Shikha

AU - Noe, Frank

AU - Noy, Agnes

AU - Oláh, Julianna

AU - O’Mara, Megan L.

AU - Ondrechen, Mary Jo

AU - Onuchic, Jose N.

AU - Onufriev, Alexey

AU - Osuna, Sílvia

AU - Palermo, Giulia

AU - Panchenko, Anna R.

AU - Pantano, Sergio

AU - Parish, Carol

AU - Parrinello, Michele

AU - Perez, Alberto

AU - Perez-Acle, Tomas

AU - Perilla, Juan R.

AU - Pettitt, B. Montgomery

AU - Pietropaolo, Adriana

AU - Piquemal, Jean Philip

AU - Poma, Adolfo B.

AU - Praprotnik, Matej

AU - Ramos, Maria J.

AU - Ren, Pengyu

AU - Reuter, Nathalie

AU - Roitberg, Adrian

AU - Rosta, Edina

AU - Rovira, Carme

AU - Roux, Benoit

AU - Rothlisberger, Ursula

AU - Sanbonmatsu, Karissa Y.

AU - Schlick, Tamar

AU - Shaytan, Alexey K.

AU - Simmerling, Carlos

AU - Smith, Jeremy C.

AU - Sugita, Yuji

AU - Świderek, Katarzyna

AU - Taiji, Makoto

AU - Tao, Peng

AU - Tieleman, D. Peter

AU - Tikhonova, Irina G.

AU - Tirado-Rives, Julian

AU - Tuñón, Iñaki

AU - van der Kamp, Marc W.

AU - van der Spoel, David

AU - Velankar, Sameer

AU - Voth, Gregory A.

AU - Wade, Rebecca

AU - Warshel, Ariel

AU - Welborn, Valerie Vaissier

AU - Wetmore, Stacey D.

AU - Wheeler, Travis J.

AU - Wong, Chung F.

AU - Yang, Lee Wei

AU - Zacharias, Martin

AU - Orozco, Modesto

PY - 2025/4

Y1 - 2025/4

N2 - 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.

AB - 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.

UR - https://www.scopus.com/pages/publications/105001997599

U2 - 10.1038/s41592-025-02635-0

DO - 10.1038/s41592-025-02635-0

M3 - Comment/debate

C2 - 40175561

SN - 1548-7091

VL - 22

SP - 641

EP - 645

JO - Nature Methods

JF - Nature Methods

IS - 4

M1 - 268

ER -

The need to implement FAIR principles in biomolecular simulations

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