doi: 10.1038/s41592-025-02635-0.
The need to implement FAIR principles in biomolecular simulations
Rommie E Amaro
1
, Johan Åqvist
2
, Ivet Bahar
3
4
, Federica Battistini
5
, Adam Bellaiche
6
, Daniel Beltran
7
, Philip C Biggin
8
, Massimiliano Bonomi
9
, Gregory R Bowman
10
, Richard A Bryce
11
, Giovanni Bussi
12
, Paolo Carloni
13
14
, David A Case
15
, Andrea Cavalli
16
17
, Chia-En A Chang
18
, Thomas E Cheatham 3rd
19
, Margaret S Cheung
20
21
, Christophe Chipot
22
23
24
, Lillian T Chong
25
, Preeti Choudhary
6
, G Andres Cisneros
26
27
, Cecilia Clementi
28
, Rosana Collepardo-Guevara
29
30
31
, Peter Coveney
32
33
, Roberto Covino
34
35
, T Daniel Crawford
36
37
, Matteo Dal Peraro
38
, Bert L de Groot
39
, Lucie Delemotte
40
, Marco De Vivo
41
, Jonathan W Essex
42
, Franca Fraternali
43
, Jiali Gao
44
, Josep Ll Gelpí
5
45
, Francesco L Gervasio
46
47
48
49
, Fernando D González-Nilo
50
, Helmut Grubmüller
51
, Marina G Guenza
52
, Horacio V Guzman
53
, Sarah Harris
54
, Teresa Head-Gordon
55
, Rigoberto Hernandez
56
, Adam Hospital
57
58
, Niu Huang
59
, Xuhui Huang
60
, Gerhard Hummer
61
62
, Javier Iglesias-Fernández
63
, Jan H Jensen
64
, Shantenu Jha
65
, Wanting Jiao
66
, William L Jorgensen
67
, Shina C L Kamerlin
68
69
, Syma Khalid
8
, Charles Laughton
70
, Michael Levitt
71
, Vittorio Limongelli
72
, Erik Lindahl
40
73
, Kresten Lindorff-Larsen
74
, Sharon Loverde
75
, Magnus Lundborg
40
, Yun L Luo
76
, F Javier Luque
77
78
, Charlotte I Lynch
8
, Alexander D MacKerell Jr
79
, Alessandra Magistrato
80
, Siewert J Marrink
81
, Hugh Martin
32
, J Andrew McCammon
82
83
, Kenneth Merz
84
85
, Vicent Moliner
86
, Adrian J Mulholland
87
, Sohail Murad
88
, Athi N Naganathan
89
, Shikha Nangia
90
, Frank Noe
91
92
93
94
, Agnes Noy
95
, Julianna Oláh
96
, Megan L O'Mara
97
, Mary Jo Ondrechen
98
, Jose N Onuchic
93
99
100
101
, Alexey Onufriev
102
103
104
, Sílvia Osuna
105
106
, Giulia Palermo
18
107
, Anna R Panchenko
108
109
110
, Sergio Pantano
111
112
, Carol Parish
113
, Michele Parrinello
114
, Alberto Perez
115
, Tomas Perez-Acle
116
117
, Juan R Perilla
118
, B Montgomery Pettitt
119
, Adriana Pietropaolo
120
, Jean-Philip Piquemal
121
, Adolfo B Poma
122
, Matej Praprotnik
123
124
, Maria J Ramos
125
, Pengyu Ren
126
, Nathalie Reuter
127
128
, Adrian Roitberg
115
, Edina Rosta
129
, Carme Rovira
106
130
, Benoit Roux
131
, Ursula Rothlisberger
132
, Karissa Y Sanbonmatsu
133
134
, Tamar Schlick
135
136
, Alexey K Shaytan
137
138
, Carlos Simmerling
3
139
, Jeremy C Smith
140
141
, Yuji Sugita
142
143
144
, Katarzyna Świderek
86
, Makoto Taiji
145
, Peng Tao
146
, D Peter Tieleman
147
, Irina G Tikhonova
148
, Julian Tirado-Rives
67
, Iñaki Tuñón
149
, Marc W van der Kamp
150
, David van der Spoel
2
, Sameer Velankar
6
, Gregory A Voth
151
, Rebecca Wade
152
, Ariel Warshel
153
, Valerie Vaissier Welborn
37
154
, Stacey D Wetmore
155
, Travis J Wheeler
156
, Chung F Wong
157
, Lee-Wei Yang
158
, Martin Zacharias
159
, Modesto Orozco
160
161
Affiliations
Affiliations
- 1 Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
- 2 Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
- 3 Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.
- 4 Department of Biochemistry and Cell Biology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA.
- 5 Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain.
- 6 European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
- 7 Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
- 8 Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK.
- 9 Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.
- 10 Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- 11 Division of Pharmacy and Optometry, University of Manchester, Manchester, UK.
- 12 Scuola Internazionale Superiore di Studi Avanzati-SISSA, Trieste, Italy.
- 13 Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany.
- 14 Department of Physics and Universitätsklinikum, RWTH Aachen University, Aachen, Germany.
- 15 Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ, USA.
- 16 Istituto Italiano di Tecnologia, Drug Discovery and Development, Bologna, Italy.
- 17 Centre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- 18 Department of Chemistry, University of California, Riverside, CA, USA.
- 19 Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA.
- 20 Department of Physics, University of Washington, Seattle, Washington, USA.
- 21 Pacific Northwest National Laboratory, Richland, Washington, USA.
- 22 LIA CNRS-UIUC, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France.
- 23 Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- 24 Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- 25 Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
- 26 Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA.
- 27 Department of Physics, University of Texas at Dallas, Richardson, TX, USA.
- 28 Theoretical and Computational Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany.
- 29 Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
- 30 Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- 31 Department of Genetics, University of Cambridge, Cambridge, UK.
- 32 Centre for Computational Science, University College London, London, UK.
- 33 Institute for Informatics, University of Amsterdam, Amsterdam, Netherlands.
- 34 Institute of Computer Science, Goethe University Frankfurt, Frankfurt am Main, Germany.
- 35 Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany.
- 36 Molecular Sciences Software Institute, Blacksburg, VA, USA.
- 37 Department of Chemistry, Virginia Tech, Blacksburg, VA, USA.
- 38 Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- 39 Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- 40 Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
- 41 Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Genoa, Italy.
- 42 School of Chemistry and Chemical Engineering, University of Southampton, Southampton, UK.
- 43 Institute of Structural and Molecular Biology, University College London, London, UK.
- 44 Department of Chemistry, University of Minnesota, Minneapolis, MN, USA.
- 45 Barcelona Supercomputing Center (BSC), Barcelona, Spain.
- 46 Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
- 47 Institute of Pharmaceutical Sciences of Western Switzerland, Geneva, Switzerland.
- 48 Chemistry Department, University College London, London, UK.
- 49 Swiss Bioinformatics Institute, Geneva, Switzerland.
- 50 Center for Bioinformatics and Integrative Biology (CBIB), Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.
- 51 Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany.
- 52 Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA.
- 53 Institut de Ciència de Materials de Barcelona, CSIC, Barcelona, Spain.
- 54 School of Physics and Astronomy, University of Sheffield, Sheffield, UK.
- 55 Pitzer Theory Center and Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
- 56 Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
- 57 Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. adam.hospital@irbbarcelona.org.
- 58 Spanish National Institute of Bioinformatics (INB)/ELIXIR-ES, Barcelona, Spain. adam.hospital@irbbarcelona.org.
- 59 National Institute of Biological Sciences, Beijing, China.
- 60 Department of Chemistry, Data Science Institute, University of Wisconsin-Madison, Madison, WI, USA.
- 61 Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- 62 Institute for Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany.
- 63 NBD | Nostrum Biodiscovery, Barcelona, Spain.
- 64 Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- 65 Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ, USA.
- 66 Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand.
- 67 Department of Chemistry, Yale University, New Haven, CT, USA.
- 68 Department of Chemistry, Lund University, Lund, Sweden.
- 69 School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
- 70 School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK.
- 71 Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- 72 Euler Institute, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Lugano, Switzerland.
- 73 Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
- 74 Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- 75 Department of Chemistry, College of Staten Island, The City University of New York, New York, NY, USA.
- 76 College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA.
- 77 Institute of Biomedicine, University of Barcelona, Santa Coloma de Gramanet, Spain.
- 78 Institute of Theoretical and Computational Chemistry, University of Barcelona, Santa Coloma de Gramanet, Spain.
- 79 Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
- 80 National Research Council-Institute of Material Foundry at Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
- 81 Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
- 82 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
- 83 Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- 84 Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA.
- 85 Department of Chemistry, Michigan State University, East Lansing, MI, USA.
- 86 BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón, Spain.
- 87 Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
- 88 Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, USA.
- 89 Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.
- 90 Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA.
- 91 Department of Physics, Freie Universität Berlin, Berlin, Germany.
- 92 Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
- 93 Department of Chemistry, Rice University, Houston, TX, USA.
- 94 Microsoft Research AI4Science, Berlin, Germany.
- 95 School of Physics, Engineering and Technology, University of York, York, UK.
- 96 Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary.
- 97 Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.
- 98 Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
- 99 Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
- 100 Department of Physics and Astronomy, Rice University, Houston, TX, USA.
- 101 Department of BioSciences, Rice University, Houston, TX, USA.
- 102 Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- 103 Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- 104 Center for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- 105 Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona, Spain.
- 106 Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
- 107 Department of Bioengineering, University of California Riverside, Riverside, CA, USA.
- 108 Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, Ontario, Canada.
- 109 Department of Biology and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
- 110 School of Computing, Queen's University, Kingston, Ontario, Canada.
- 111 Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- 112 Bioinformatics Area, DETEMA, Faculty of Chemistry, Udelar, Montevideo, Uruguay.
- 113 Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA, USA.
- 114 Atomistic Simulations, Italian Institute of Technology, Genova, Italy.
- 115 Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.
- 116 Computational Biology Lab, Fundación Ciencia & Vida, Santiago, Chile.
- 117 Facultad de Ingeniería, Universidad San Sebastián, Santiago, Chile.
- 118 Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.
- 119 University of Texas Medical Branch, Galveston, TX, USA.
- 120 Dipartimento di Scienze della Salute, Università di Catanzaro, Catanzaro, Italy.
- 121 Laboratory of Theoretical Chemistry, Department of Chemistry, Sorbonne University, Paris, France.
- 122 Biosystems and Soft Matter Division, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland.
- 123 Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia.
- 124 Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia.
- 125 Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal.
- 126 Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
- 127 Department of Chemistry, University of Bergen, Bergen, Norway.
- 128 Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
- 129 Department of Physics and Astronomy, University College London, London, UK.
- 130 Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain.
- 131 Department of Chemistry, University of Chicago, Chicago, IL, USA.
- 132 Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- 133 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.
- 134 New Mexico Consortium, Los Alamos, NM, USA.
- 135 Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.
- 136 Simons Center for Computational Physical Chemistry, New York University, New York, NY, USA.
- 137 Department of Biology, Lomonosov Moscow State University, Moscow, Russia.
- 138 International Laboratory of Bioinformatics, AI and Digital Sciences Institute, Faculty of Computer Science, HSE University, Moscow, Russia.
- 139 Department of Chemistry, Stony Brook University, Stony Brook, NY, USA.
- 140 Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- 141 Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.
- 142 Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan.
- 143 Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan.
- 144 Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
- 145 Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
- 146 Department of Chemistry, O'Donnell Data Science and Research Computing Institute, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, USA.
- 147 Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada.
- 148 School of Pharmacy, Queen's University Belfast, Belfast, UK.
- 149 Departamento de Química Física, Universidad de Valencia, Burjassot, Spain.
- 150 School of Biochemistry, University of Bristol, Bristol, UK.
- 151 Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL, USA.
- 152 Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
- 153 Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
- 154 Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA, USA.
- 155 Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
- 156 R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona, USA.
- 157 Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, MO, USA.
- 158 Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.
- 159 Physics Department, Technical University of Munich, Garching, Germany.
- 160 Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain. modesto.orozco@irbbarcelona.org.
- 161 Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. modesto.orozco@irbbarcelona.org.
- PMID: 40175561
- DOI: 10.1038/s41592-025-02635-0
Item in Clipboard
The need to implement FAIR principles in biomolecular simulations
Rommie E Amaro et al.
Nat Methods.
2025 Apr.
Free article
Display options
Format
doi: 10.1038/s41592-025-02635-0.
Authors
Rommie E Amaro
1
, Johan Åqvist
2
, Ivet Bahar
3
4
, Federica Battistini
5
, Adam Bellaiche
6
, Daniel Beltran
7
, Philip C Biggin
8
, Massimiliano Bonomi
9
, Gregory R Bowman
10
, Richard A Bryce
11
, Giovanni Bussi
12
, Paolo Carloni
13
14
, David A Case
15
, Andrea Cavalli
16
17
, Chia-En A Chang
18
, Thomas E Cheatham 3rd
19
, Margaret S Cheung
20
21
, Christophe Chipot
22
23
24
, Lillian T Chong
25
, Preeti Choudhary
6
, G Andres Cisneros
26
27
, Cecilia Clementi
28
, Rosana Collepardo-Guevara
29
30
31
, Peter Coveney
32
33
, Roberto Covino
34
35
, T Daniel Crawford
36
37
, Matteo Dal Peraro
38
, Bert L de Groot
39
, Lucie Delemotte
40
, Marco De Vivo
41
, Jonathan W Essex
42
, Franca Fraternali
43
, Jiali Gao
44
, Josep Ll Gelpí
5
45
, Francesco L Gervasio
46
47
48
49
, Fernando D González-Nilo
50
, Helmut Grubmüller
51
, Marina G Guenza
52
, Horacio V Guzman
53
, Sarah Harris
54
, Teresa Head-Gordon
55
, Rigoberto Hernandez
56
, Adam Hospital
57
58
, Niu Huang
59
, Xuhui Huang
60
, Gerhard Hummer
61
62
, Javier Iglesias-Fernández
63
, Jan H Jensen
64
, Shantenu Jha
65
, Wanting Jiao
66
, William L Jorgensen
67
, Shina C L Kamerlin
68
69
, Syma Khalid
8
, Charles Laughton
70
, Michael Levitt
71
, Vittorio Limongelli
72
, Erik Lindahl
40
73
, Kresten Lindorff-Larsen
74
, Sharon Loverde
75
, Magnus Lundborg
40
, Yun L Luo
76
, F Javier Luque
77
78
, Charlotte I Lynch
8
, Alexander D MacKerell Jr
79
, Alessandra Magistrato
80
, Siewert J Marrink
81
, Hugh Martin
32
, J Andrew McCammon
82
83
, Kenneth Merz
84
85
, Vicent Moliner
86
, Adrian J Mulholland
87
, Sohail Murad
88
, Athi N Naganathan
89
, Shikha Nangia
90
, Frank Noe
91
92
93
94
, Agnes Noy
95
, Julianna Oláh
96
, Megan L O'Mara
97
, Mary Jo Ondrechen
98
, Jose N Onuchic
93
99
100
101
, Alexey Onufriev
102
103
104
, Sílvia Osuna
105
106
, Giulia Palermo
18
107
, Anna R Panchenko
108
109
110
, Sergio Pantano
111
112
, Carol Parish
113
, Michele Parrinello
114
, Alberto Perez
115
, Tomas Perez-Acle
116
117
, Juan R Perilla
118
, B Montgomery Pettitt
119
, Adriana Pietropaolo
120
, Jean-Philip Piquemal
121
, Adolfo B Poma
122
, Matej Praprotnik
123
124
, Maria J Ramos
125
, Pengyu Ren
126
, Nathalie Reuter
127
128
, Adrian Roitberg
115
, Edina Rosta
129
, Carme Rovira
106
130
, Benoit Roux
131
, Ursula Rothlisberger
132
, Karissa Y Sanbonmatsu
133
134
, Tamar Schlick
135
136
, Alexey K Shaytan
137
138
, Carlos Simmerling
3
139
, Jeremy C Smith
140
141
, Yuji Sugita
142
143
144
, Katarzyna Świderek
86
, Makoto Taiji
145
, Peng Tao
146
, D Peter Tieleman
147
, Irina G Tikhonova
148
, Julian Tirado-Rives
67
, Iñaki Tuñón
149
, Marc W van der Kamp
150
, David van der Spoel
2
, Sameer Velankar
6
, Gregory A Voth
151
, Rebecca Wade
152
, Ariel Warshel
153
, Valerie Vaissier Welborn
37
154
, Stacey D Wetmore
155
, Travis J Wheeler
156
, Chung F Wong
157
, Lee-Wei Yang
158
, Martin Zacharias
159
, Modesto Orozco
160
161
Affiliations
- 1 Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA.
- 2 Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
- 3 Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.
- 4 Department of Biochemistry and Cell Biology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA.
- 5 Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain.
- 6 European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
- 7 Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
- 8 Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK.
- 9 Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.
- 10 Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.
- 11 Division of Pharmacy and Optometry, University of Manchester, Manchester, UK.
- 12 Scuola Internazionale Superiore di Studi Avanzati-SISSA, Trieste, Italy.
- 13 Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany.
- 14 Department of Physics and Universitätsklinikum, RWTH Aachen University, Aachen, Germany.
- 15 Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ, USA.
- 16 Istituto Italiano di Tecnologia, Drug Discovery and Development, Bologna, Italy.
- 17 Centre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- 18 Department of Chemistry, University of California, Riverside, CA, USA.
- 19 Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA.
- 20 Department of Physics, University of Washington, Seattle, Washington, USA.
- 21 Pacific Northwest National Laboratory, Richland, Washington, USA.
- 22 LIA CNRS-UIUC, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France.
- 23 Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- 24 Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- 25 Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
- 26 Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA.
- 27 Department of Physics, University of Texas at Dallas, Richardson, TX, USA.
- 28 Theoretical and Computational Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany.
- 29 Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
- 30 Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- 31 Department of Genetics, University of Cambridge, Cambridge, UK.
- 32 Centre for Computational Science, University College London, London, UK.
- 33 Institute for Informatics, University of Amsterdam, Amsterdam, Netherlands.
- 34 Institute of Computer Science, Goethe University Frankfurt, Frankfurt am Main, Germany.
- 35 Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany.
- 36 Molecular Sciences Software Institute, Blacksburg, VA, USA.
- 37 Department of Chemistry, Virginia Tech, Blacksburg, VA, USA.
- 38 Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- 39 Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
- 40 Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
- 41 Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Genoa, Italy.
- 42 School of Chemistry and Chemical Engineering, University of Southampton, Southampton, UK.
- 43 Institute of Structural and Molecular Biology, University College London, London, UK.
- 44 Department of Chemistry, University of Minnesota, Minneapolis, MN, USA.
- 45 Barcelona Supercomputing Center (BSC), Barcelona, Spain.
- 46 Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.
- 47 Institute of Pharmaceutical Sciences of Western Switzerland, Geneva, Switzerland.
- 48 Chemistry Department, University College London, London, UK.
- 49 Swiss Bioinformatics Institute, Geneva, Switzerland.
- 50 Center for Bioinformatics and Integrative Biology (CBIB), Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.
- 51 Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany.
- 52 Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA.
- 53 Institut de Ciència de Materials de Barcelona, CSIC, Barcelona, Spain.
- 54 School of Physics and Astronomy, University of Sheffield, Sheffield, UK.
- 55 Pitzer Theory Center and Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.
- 56 Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
- 57 Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. adam.hospital@irbbarcelona.org.
- 58 Spanish National Institute of Bioinformatics (INB)/ELIXIR-ES, Barcelona, Spain. adam.hospital@irbbarcelona.org.
- 59 National Institute of Biological Sciences, Beijing, China.
- 60 Department of Chemistry, Data Science Institute, University of Wisconsin-Madison, Madison, WI, USA.
- 61 Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- 62 Institute for Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany.
- 63 NBD | Nostrum Biodiscovery, Barcelona, Spain.
- 64 Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- 65 Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ, USA.
- 66 Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand.
- 67 Department of Chemistry, Yale University, New Haven, CT, USA.
- 68 Department of Chemistry, Lund University, Lund, Sweden.
- 69 School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
- 70 School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK.
- 71 Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- 72 Euler Institute, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Lugano, Switzerland.
- 73 Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.
- 74 Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- 75 Department of Chemistry, College of Staten Island, The City University of New York, New York, NY, USA.
- 76 College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA.
- 77 Institute of Biomedicine, University of Barcelona, Santa Coloma de Gramanet, Spain.
- 78 Institute of Theoretical and Computational Chemistry, University of Barcelona, Santa Coloma de Gramanet, Spain.
- 79 Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
- 80 National Research Council-Institute of Material Foundry at Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
- 81 Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
- 82 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.
- 83 Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- 84 Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA.
- 85 Department of Chemistry, Michigan State University, East Lansing, MI, USA.
- 86 BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón, Spain.
- 87 Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
- 88 Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, USA.
- 89 Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.
- 90 Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA.
- 91 Department of Physics, Freie Universität Berlin, Berlin, Germany.
- 92 Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.
- 93 Department of Chemistry, Rice University, Houston, TX, USA.
- 94 Microsoft Research AI4Science, Berlin, Germany.
- 95 School of Physics, Engineering and Technology, University of York, York, UK.
- 96 Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary.
- 97 Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.
- 98 Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
- 99 Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.
- 100 Department of Physics and Astronomy, Rice University, Houston, TX, USA.
- 101 Department of BioSciences, Rice University, Houston, TX, USA.
- 102 Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- 103 Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- 104 Center for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
- 105 Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona, Spain.
- 106 Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
- 107 Department of Bioengineering, University of California Riverside, Riverside, CA, USA.
- 108 Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, Ontario, Canada.
- 109 Department of Biology and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
- 110 School of Computing, Queen's University, Kingston, Ontario, Canada.
- 111 Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- 112 Bioinformatics Area, DETEMA, Faculty of Chemistry, Udelar, Montevideo, Uruguay.
- 113 Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA, USA.
- 114 Atomistic Simulations, Italian Institute of Technology, Genova, Italy.
- 115 Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.
- 116 Computational Biology Lab, Fundación Ciencia & Vida, Santiago, Chile.
- 117 Facultad de Ingeniería, Universidad San Sebastián, Santiago, Chile.
- 118 Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.
- 119 University of Texas Medical Branch, Galveston, TX, USA.
- 120 Dipartimento di Scienze della Salute, Università di Catanzaro, Catanzaro, Italy.
- 121 Laboratory of Theoretical Chemistry, Department of Chemistry, Sorbonne University, Paris, France.
- 122 Biosystems and Soft Matter Division, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland.
- 123 Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia.
- 124 Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia.
- 125 Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal.
- 126 Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
- 127 Department of Chemistry, University of Bergen, Bergen, Norway.
- 128 Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway.
- 129 Department of Physics and Astronomy, University College London, London, UK.
- 130 Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain.
- 131 Department of Chemistry, University of Chicago, Chicago, IL, USA.
- 132 Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
- 133 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.
- 134 New Mexico Consortium, Los Alamos, NM, USA.
- 135 Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.
- 136 Simons Center for Computational Physical Chemistry, New York University, New York, NY, USA.
- 137 Department of Biology, Lomonosov Moscow State University, Moscow, Russia.
- 138 International Laboratory of Bioinformatics, AI and Digital Sciences Institute, Faculty of Computer Science, HSE University, Moscow, Russia.
- 139 Department of Chemistry, Stony Brook University, Stony Brook, NY, USA.
- 140 Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- 141 Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.
- 142 Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan.
- 143 Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan.
- 144 Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
- 145 Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
- 146 Department of Chemistry, O'Donnell Data Science and Research Computing Institute, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, USA.
- 147 Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada.
- 148 School of Pharmacy, Queen's University Belfast, Belfast, UK.
- 149 Departamento de Química Física, Universidad de Valencia, Burjassot, Spain.
- 150 School of Biochemistry, University of Bristol, Bristol, UK.
- 151 Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL, USA.
- 152 Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
- 153 Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
- 154 Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA, USA.
- 155 Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
- 156 R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona, USA.
- 157 Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, MO, USA.
- 158 Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.
- 159 Physics Department, Technical University of Munich, Garching, Germany.
- 160 Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain. modesto.orozco@irbbarcelona.org.
- 161 Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. modesto.orozco@irbbarcelona.org.
- PMID: 40175561
- DOI: 10.1038/s41592-025-02635-0
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Conflict of interest statement
Competing interests: The authors declare no competing interests.
References
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- wwPDB Consortium. Nucleic Acids Res. 47, D520–D528 (2019). (D1). - DOI
