The need to implement FAIR principles in biomolecular simulations.

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Title: The need to implement FAIR principles in biomolecular simulations.
Authors: Amaro RE; Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA., Åqvist J; Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden., Bahar I; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.; Department of Biochemistry and Cell Biology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA., Battistini F; Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain., Bellaiche A; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK., Beltran D; Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain., Biggin PC; Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK., Bonomi M; Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France., Bowman GR; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA., Bryce RA; Division of Pharmacy and Optometry, University of Manchester, Manchester, UK., Bussi G; Scuola Internazionale Superiore di Studi Avanzati-SISSA, Trieste, Italy., Carloni P; Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany.; Department of Physics and Universitätsklinikum, RWTH Aachen University, Aachen, Germany., Case DA; Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ, USA., Cavalli A; Istituto Italiano di Tecnologia, Drug Discovery and Development, Bologna, Italy.; Centre Européen de Calcul Atomique et Moléculaire (CECAM), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland., Chang CA; Department of Chemistry, University of California, Riverside, CA, USA., Cheatham TE 3rd; Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA., Cheung MS; Department of Physics, University of Washington, Seattle, Washington, USA.; Pacific Northwest National Laboratory, Richland, Washington, USA., Chipot C; LIA CNRS-UIUC, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France.; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA., Chong LT; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA., Choudhary P; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK., Cisneros GA; Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA.; Department of Physics, University of Texas at Dallas, Richardson, TX, USA., Clementi C; Theoretical and Computational Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany., Collepardo-Guevara R; Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.; Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.; Department of Genetics, University of Cambridge, Cambridge, UK., Coveney P; Centre for Computational Science, University College London, London, UK.; Institute for Informatics, University of Amsterdam, Amsterdam, Netherlands., Covino R; Institute of Computer Science, Goethe University Frankfurt, Frankfurt am Main, Germany.; Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany., Crawford TD; Molecular Sciences Software Institute, Blacksburg, VA, USA.; Department of Chemistry, Virginia Tech, Blacksburg, VA, USA., Dal Peraro M; Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland., de Groot BL; Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany., Delemotte L; Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden., De Vivo M; Laboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Genoa, Italy., Essex JW; School of Chemistry and Chemical Engineering, University of Southampton, Southampton, UK., Fraternali F; Institute of Structural and Molecular Biology, University College London, London, UK., Gao J; Department of Chemistry, University of Minnesota, Minneapolis, MN, USA., Gelpí JL; Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain.; Barcelona Supercomputing Center (BSC), Barcelona, Spain., Gervasio FL; Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.; Institute of Pharmaceutical Sciences of Western Switzerland, Geneva, Switzerland.; Chemistry Department, University College London, London, UK.; Swiss Bioinformatics Institute, Geneva, Switzerland., González-Nilo FD; Center for Bioinformatics and Integrative Biology (CBIB), Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile., Grubmüller H; Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany., Guenza MG; Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA., Guzman HV; Institut de Ciència de Materials de Barcelona, CSIC, Barcelona, Spain., Harris S; School of Physics and Astronomy, University of Sheffield, Sheffield, UK., Head-Gordon T; Pitzer Theory Center and Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA., Hernandez R; Department of Chemistry, Johns Hopkins University, Baltimore, MD, USA., Hospital A; Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. adam.hospital@irbbarcelona.org.; Spanish National Institute of Bioinformatics (INB)/ELIXIR-ES, Barcelona, Spain. adam.hospital@irbbarcelona.org., Huang N; National Institute of Biological Sciences, Beijing, China., Huang X; Department of Chemistry, Data Science Institute, University of Wisconsin-Madison, Madison, WI, USA., Hummer G; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.; Institute for Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany., Iglesias-Fernández J; NBD | Nostrum Biodiscovery, Barcelona, Spain., Jensen JH; Department of Chemistry, University of Copenhagen, Copenhagen, Denmark., Jha S; Department of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ, USA., Jiao W; Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand., Jorgensen WL; Department of Chemistry, Yale University, New Haven, CT, USA., Kamerlin SCL; Department of Chemistry, Lund University, Lund, Sweden.; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA., Khalid S; Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK., Laughton C; School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK., Levitt M; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA., Limongelli V; Euler Institute, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Lugano, Switzerland., Lindahl E; Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.; Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden., Lindorff-Larsen K; Structural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark., Loverde S; Department of Chemistry, College of Staten Island, The City University of New York, New York, NY, USA., Lundborg M; Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden., Luo YL; College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA., Luque FJ; Institute of Biomedicine, University of Barcelona, Santa Coloma de Gramanet, Spain.; Institute of Theoretical and Computational Chemistry, University of Barcelona, Santa Coloma de Gramanet, Spain., Lynch CI; Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK., MacKerell AD Jr; Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA., Magistrato A; National Research Council-Institute of Material Foundry at Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy., Marrink SJ; Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands., Martin H; Centre for Computational Science, University College London, London, UK., McCammon JA; Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.; Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA., Merz K; Lerner Research Institute Cleveland Clinic, Cleveland, OH, USA.; Department of Chemistry, Michigan State University, East Lansing, MI, USA., Moliner V; BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón, Spain., Mulholland AJ; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK., Murad S; Department of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, USA., Naganathan AN; Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India., Nangia S; Department of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA., Noe F; Department of Physics, Freie Universität Berlin, Berlin, Germany.; Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany.; Department of Chemistry, Rice University, Houston, TX, USA.; Microsoft Research AI4Science, Berlin, Germany., Noy A; School of Physics, Engineering and Technology, University of York, York, UK., Oláh J; Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary., O'Mara ML; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia., Ondrechen MJ; Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA., Onuchic JN; Department of Chemistry, Rice University, Houston, TX, USA.; Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.; Department of Physics and Astronomy, Rice University, Houston, TX, USA.; Department of BioSciences, Rice University, Houston, TX, USA., Onufriev A; Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.; Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.; Center for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA., Osuna S; Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona, Spain.; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain., Palermo G; Department of Chemistry, University of California, Riverside, CA, USA.; Department of Bioengineering, University of California Riverside, Riverside, CA, USA., Panchenko AR; Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, Ontario, Canada.; Department of Biology and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.; School of Computing, Queen's University, Kingston, Ontario, Canada., Pantano S; Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo, Uruguay.; Bioinformatics Area, DETEMA, Faculty of Chemistry, Udelar, Montevideo, Uruguay., Parish C; Department of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA, USA., Parrinello M; Atomistic Simulations, Italian Institute of Technology, Genova, Italy., Perez A; Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA., Perez-Acle T; Computational Biology Lab, Fundación Ciencia & Vida, Santiago, Chile.; Facultad de Ingeniería, Universidad San Sebastián, Santiago, Chile., Perilla JR; Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA., Pettitt BM; University of Texas Medical Branch, Galveston, TX, USA., Pietropaolo A; Dipartimento di Scienze della Salute, Università di Catanzaro, Catanzaro, Italy., Piquemal JP; Laboratory of Theoretical Chemistry, Department of Chemistry, Sorbonne University, Paris, France., Poma AB; Biosystems and Soft Matter Division, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland., Praprotnik M; Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia.; Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia., Ramos MJ; Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal., Ren P; Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA., Reuter N; Department of Chemistry, University of Bergen, Bergen, Norway.; Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway., Roitberg A; Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA., Rosta E; Department of Physics and Astronomy, University College London, London, UK., Rovira C; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.; Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain., Roux B; Department of Chemistry, University of Chicago, Chicago, IL, USA., Rothlisberger U; Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland., Sanbonmatsu KY; Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.; New Mexico Consortium, Los Alamos, NM, USA., Schlick T; Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.; Simons Center for Computational Physical Chemistry, New York University, New York, NY, USA., Shaytan AK; Department of Biology, Lomonosov Moscow State University, Moscow, Russia.; International Laboratory of Bioinformatics, AI and Digital Sciences Institute, Faculty of Computer Science, HSE University, Moscow, Russia., Simmerling C; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA., Smith JC; Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA.; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA., Sugita Y; Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan.; Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Saitama, Japan.; Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan., Świderek K; BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón, Spain., Taiji M; Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan., Tao P; 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., Tieleman DP; Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada., Tikhonova IG; School of Pharmacy, Queen's University Belfast, Belfast, UK., Tirado-Rives J; Department of Chemistry, Yale University, New Haven, CT, USA., Tuñón I; Departamento de Química Física, Universidad de Valencia, Burjassot, Spain., van der Kamp MW; School of Biochemistry, University of Bristol, Bristol, UK., van der Spoel D; Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden., Velankar S; European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK., Voth GA; Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL, USA., Wade R; Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany., Warshel A; Department of Chemistry, University of Southern California, Los Angeles, CA, USA., Welborn VV; Department of Chemistry, Virginia Tech, Blacksburg, VA, USA.; Macromolecules Innovation Institute, Virginia Tech, Blacksburg, VA, USA., Wetmore SD; Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada., Wheeler TJ; R. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona, USA., Wong CF; Department of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, MO, USA., Yang LW; Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan., Zacharias M; Physics Department, Technical University of Munich, Garching, Germany., Orozco M; Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain. modesto.orozco@irbbarcelona.org.; Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. modesto.orozco@irbbarcelona.org.
Source: Nature methods [Nat Methods] 2025 Apr; Vol. 22 (4), pp. 641-645.
Publication Type: Journal Article
Journal Info: Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101215604 Publication Model: Print Cited Medium: Internet ISSN: 1548-7105 (Electronic) Linking ISSN: 15487091 NLM ISO Abbreviation: Nat Methods Subsets: MEDLINE; In Process
Database: MEDLINE Ultimate
Description
ISSN:1548-7105
DOI:10.1038/s41592-025-02635-0