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
Authors 92
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University of California San Diego
Affiliation as printed
UC San Diego - University of California [San Diego] (UCSD, 9500 Gilman Dr., La Jolla, CA 92093 USA - United States)
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Affiliation as printed
Uppsala University (Box 256, SE-751 05 Uppsala - Sweden)
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Affiliation as printed
SBU - Stony Brook University [SUNY] (100 Nicolls Road, Stony Brook, NY 11794 - United States)
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Institute for Research in Biomedicine
Affiliation as printed
IRB - Institute for Research in Biomedicine [Barcelona, Spain] (Parc Científic de Barcelona C/ Baldiri Reixac 10 08028 Barcelona - Spain)
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European Bioinformatics Institute
Affiliation as printed
EMBL-EBI - European Bioinformatics Institute [Hinxton] (EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK - United Kingdom)
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Institute for Research in Biomedicine
Affiliation as printed
IRB - Institute for Research in Biomedicine [Barcelona, Spain] (Parc Científic de Barcelona C/ Baldiri Reixac 10 08028 Barcelona - Spain)
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Affiliation as printed
University of Oxford (Wellington Square, Oxford OX1 2JD - United Kingdom)
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Affiliation as printed
Département de Biologie structurale et Chimie - Department of Structural Biology and Chemistry (25-28 rue du Docteur Roux, 75724 Paris cedex 15 - France)
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Affiliation as printed
University of Pennsylvania (3451 Walnut Street, Philadelphia, PA 19104 | 215-898-5000 - United States)
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Affiliation as printed
University of Manchester [Manchester] (Oxford Rd, Manchester M13 9PL - United Kingdom)
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Giovanni Bussi Aachen
Scuola Internazionale Superiore di Studi Avanzati · Universitätsklinikum Aachen · RWTH Aachen University
Affiliation as printed
SISSA / ISAS - Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies (via Bonomea, 265 - 34136 Trieste - Italy - Italy)
UKA - Universitätsklinikum RWTH Aachen - University Hospital Aachen [Aachen, Germany] (Universitätsklinikum Aachen, AöR - Pauwelsstraße 30 - 52074 Aachen - Germany)
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Paolo Carloni Aachen
Forschungszentrum Jülich · Universitätsklinikum Aachen · RWTH Aachen University
Affiliation as printed
Forschungszentrum Jülich
FZJ - Forschungszentrum Jülich GmbH | Centre de recherche de Jülich | Jülich Research Centre (Wilhelm-Johnen-Straße, 52428 Jülich - Germany)
UKA - Universitätsklinikum RWTH Aachen - University Hospital Aachen [Aachen, Germany] (Universitätsklinikum Aachen, AöR - Pauwelsstraße 30 - 52074 Aachen - Germany)
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Rutgers, The State University of New Jersey
Affiliation as printed
Rutgers - Rutgers University System (Camden, Newark, New Brunswick, New Jersey - United States)
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Italian Institute of Technology
Affiliation as printed
CECAM - Centre Européen de Calcul Atomique et Moléculaire (France)
IIT - Italian Institute of Technology = Istituto Italiano di Tecnologia (Istituto Italiano di Tecnologia (IIT). Via Morego 30 16163 Genova, Italy - Italy)
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University of California, Riverside
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UC Riverside - University of California [Riverside] (900 University Ave. Riverside, CA 92521 - United States)
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Affiliation as printed
University of Utah (201 Presidents Cir, Salt Lake City, UT 84112 - United States)
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Pacific Northwest National Laboratory · University of Washington · University of Chicago
Affiliation as printed
PNNL - Pacific Northwest National Laboratory (Richland, WA 99352 - United States)
University of Chicago (Edward H. Levi Hall 5801 South Ellis Avenue Chicago, Illinois 60637 - United States)
University of Washington [Seattle] (Seattle, Washington 98105 - United States)
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University of Illinois Urbana-Champaign · University of Chicago · Laboratoire de Physique et Chimie Théoriques
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LPCT - Laboratoire de Physique et Chimie Théoriques (Boulevard des Aiguillettes - B.P. 70239 F-54506 Vandoeuvre-les-Nancy - France)
UIUC - University of Illinois at Urbana-Champaign [Urbana] (205 N. Mathews Ave., Urbana-Champaign, IL 61801 - United States)
University of Chicago (Edward H. Levi Hall 5801 South Ellis Avenue Chicago, Illinois 60637 - United States)
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Affiliation as printed
PITT - University of Pittsburgh (4200 Fifth Avenue Pittsburgh, PA 15260 - United States)
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European Bioinformatics Institute
Affiliation as printed
EMBL-EBI - European Bioinformatics Institute [Hinxton] (EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK - United Kingdom)
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Affiliation as printed
Freie Universität Berlin (Kaiserswerther Str. 16-18, 14195 Berlin - Germany)
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University of Cambridge · Cambridge University Press
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CAM - University of Cambridge [UK] (The Old Schools, Trinity Lane, Cambridge CB2 1TN - United Kingdom)
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University College London · University of Amsterdam
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UCL - University College of London [London] (Gower Street, London WC1E 6BT - United Kingdom)
UvA - University of Amsterdam [Amsterdam] = Universiteit van Amsterdam (Spui 21 1012 WX Amsterdam - Netherlands)
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Molecular Sciences Software Institute · Virginia Tech
Affiliation as printed
MolSSI - Molecular Sciences Software Institute [Blacksburg, USA] (1880 Pratt Dr #1100 Blacksburg, VA 24060 - United States)
Virginia Tech [Blacksburg] (Virginia Polytechnic Institute and State University Blacksburg, VA 24061-0002 - United States)
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Max Planck Society · Max Planck Institute for Multidisciplinary Sciences
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Max Planck Institute for Multidisciplinary Sciences / Max-Planck-Institut für Multidisziplinäre Naturwissenschaften [Göttingen, Germany] (Germany)
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Universidad Autónoma de Madrid
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UAM - Universidad Autónoma de Madrid (Ciudad Universitaria de Cantoblanco · 28049 Madrid - Spain)
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KTH Royal Institute of Technology
Affiliation as printed
KTH - KTH Royal Institute of Technology [Stockholm] (SE-100 44, Stockholm, Sweden - Sweden)
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Italian Institute of Technology
Affiliation as printed
IIT - Italian Institute of Technology = Istituto Italiano di Tecnologia (Istituto Italiano di Tecnologia (IIT). Via Morego 30 16163 Genova, Italy - Italy)
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Affiliation as printed
University of Southampton (University Road, Southampton SO17 1BJ - United Kingdom)
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Affiliation as printed
UCL - University College of London [London] (Gower Street, London WC1E 6BT - United Kingdom)
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Affiliation as printed
UMN - University of Minnesota [Twin Cities] (Minneapolis, MN 55455 - United States)
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Barcelona Supercomputing Center · Universitat de Barcelona
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BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (Plaça d'Eusebi Güell, 1-3, Les Corts, 08034 Barcelona - Spain)
UB - Universitat de Barcelona (Gran Via de les Corts Catalanes, 585, 08007 Barcelona - Spain)
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University of Geneva · SIB Swiss Institute of Bioinformatics · University College London
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SIB - Swiss Institute of Bioinformatics [Genève] (rue Michel-Servet 1, 1211 Geneva 4 - Switzerland)
UCL - University College of London [London] (Gower Street, London WC1E 6BT - United Kingdom)
UNIGE - Université de Genève = University of Geneva (24 rue du Général-Dufour CH - 1211 Genève 4 Suisse - Switzerland)
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Affiliation as printed
UNAB - Universidad Andrés Bello [Santiago] (República 239 Santiago CHILE - Chile)
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Max Planck Society · Max Planck Institute for Multidisciplinary Sciences
Affiliation as printed
Max Planck Institute for Multidisciplinary Sciences / Max-Planck-Institut für Multidisziplinäre Naturwissenschaften [Göttingen, Germany] (Germany)
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Affiliation as printed
University of Sheffield [Sheffield] (Western Bank Sheffield S10 2TN - United Kingdom)
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University of California, Berkeley
Affiliation as printed
UC Berkeley - University of California [Berkeley] (Berkeley, CA - United States)
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Affiliation as printed
JHU - Johns Hopkins University (Baltimore, Maryland 410-516-8000 - United States)
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Institute for Research in Biomedicine
Affiliation as printed
INB-ISCIII - Instituto Nacional de Bioinformática = Spanish National Bioinformatics Institute [Barcelona, Spain] (Spain)
IRB - Institute for Research in Biomedicine [Barcelona, Spain] (Parc Científic de Barcelona C/ Baldiri Reixac 10 08028 Barcelona - Spain)
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National Institute of Biological Sciences, Beijing
Affiliation as printed
NIBS - National Institute of Biological Sciences [Beijing, China] (7 Science Park Road ZGC Life Science Park, Beijing 102206 - China)
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University of Wisconsin–Madison
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University of Wisconsin-Madison (Madison, WI 53706 - United States)
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Goethe University Frankfurt · Max Planck Institute of Biophysics
Affiliation as printed
Goethe University Frankfurt (Theodor-W.-Adorno-Platz 1 , 60323 Frankfurt am Main - Germany)
MPIBP - Max-Planck-Institut für Biophysik - Max Planck Institute of Biophysics [Frankfurt am Main, Germany] (Max-von-Laue-Strasse 3, 60438 Frankfurt am Main - Germany)
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NBD - Nostrum Biodiscovery [Barcelona, Spain] (Av. Josep Tarradellas 8-10, 3º 2ª, 08029, Barcelona - Spain)
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Affiliation as printed
UCPH - University of Copenhagen = Københavns Universitet (Nørregade 10, 1165 København, Danemark - Denmark)
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Rutgers, The State University of New Jersey
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Rutgers - Rutgers University System (Camden, Newark, New Brunswick, New Jersey - United States)
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Victoria University of Wellington
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Victoria University of Wellington (PO Box 600 Wellington 6140 NEW ZEALAND - New Zealand)
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Uppsala University · Georgia Institute of Technology
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Georgia Institute of Technology [Atlanta] (North Avenue, Atlanta, GA 30332 - United States)
Uppsala University (Box 256, SE-751 05 Uppsala - Sweden)
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Affiliation as printed
University of Oxford (Wellington Square, Oxford OX1 2JD - United Kingdom)
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Stanford University (450 Serra Mall, Stanford, CA 94305-2004 - United States)
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Università della Svizzera italiana
Affiliation as printed
USI - Università della Svizzera italiana = University of Italian Switzerland (Via Giuseppe Buffi 13, 6900 Lugano, Suisse - Switzerland)
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Stockholm University · KTH Royal Institute of Technology
Affiliation as printed
KTH - KTH Royal Institute of Technology [Stockholm] (SE-100 44, Stockholm, Sweden - Sweden)
Stockholm University (SE-106 91 Stockholm - Sweden)
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Affiliation as printed
UCPH - University of Copenhagen = Københavns Universitet (Nørregade 10, 1165 København, Danemark - Denmark)
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Affiliation as printed
CUNY - City University of New York [New York] (217 East 42 St, New York, NY 10017 - United States)
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KTH Royal Institute of Technology
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KTH - KTH Royal Institute of Technology [Stockholm] (SE-100 44, Stockholm, Sweden - Sweden)
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Affiliation as printed
UB - Universitat de Barcelona (Gran Via de les Corts Catalanes, 585, 08007 Barcelona - Spain)
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Affiliation as printed
University of Oxford (Wellington Square, Oxford OX1 2JD - United Kingdom)
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University of Maryland, Baltimore
Affiliation as printed
University of Maryland [Baltimore] (Baltimore, MD 21201 - United States)
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Scuola Internazionale Superiore di Studi Avanzati
Affiliation as printed
SISSA / ISAS - Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies (via Bonomea, 265 - 34136 Trieste - Italy - Italy)
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Affiliation as printed
University of Groningen [Groningen] (PO Box 72 , 9700 AB Groningen - Netherlands)
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Affiliation as printed
UCL - University College of London [London] (Gower Street, London WC1E 6BT - United Kingdom)
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University of California San Diego
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UC San Diego - University of California [San Diego] (UCSD, 9500 Gilman Dr., La Jolla, CA 92093 USA - United States)
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Cleveland Clinic Lerner College of Medicine · Michigan State University
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Lerner Research Institute [Cleveland, OH, USA] (Lerner Research Institute - 9500 Euclid Avenue, NB21 Cleveland, OH 44195 - United States)
Michigan State University System (Michigan - United States)
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Universitat Jaume I = Jaume I University (Universitat Jaume I Av. de Vicent Sos Baynat s/n 12071 Castelló de la Plana CIF:Q-6250003-H - Spain)
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University of Bristol [Bristol] (Senate House, Tyndall Avenue, Bristol BS8 1TH - United Kingdom)
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Illinois Institute of Technology
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IIT - Illinois Institute of Technology (Chicago, IL 60616 - United States)
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Indian Institute of Technology Madras
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IIT Madras - Indian Institute of Technology Madras (Chennai 600036 - India)
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Syracuse University (900 South Crouse Ave Syracuse, NY 13244 - United States)
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Microsoft (Germany) · Rice University · Freie Universität Berlin
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Freie Universität Berlin (Kaiserswerther Str. 16-18, 14195 Berlin - Germany)
MSR AI4Sciences - Microsoft Research AI4Science [Berlin,Germany] (Berlin - Germany)
Rice University [Houston] (P.O. Box 1892, Houston, Texas 77251-1892 - United States)
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Affiliation as printed
University of York [York, UK] (Heslington, York, YO10 5DD - United Kingdom)
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Budapest University of Technology and Economics
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BME - Budapest University of Technology and Economics [Budapest] (Műegyetem rkp. 3, 1111 - Budapest - Hungary)
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Affiliation as printed
UQ [All campuses : Brisbane, Dutton Park Gatton, Herston, St Lucia and other locations] - The University of Queensland (Brisbane, St Lucia, QLD 4072 - Australia)
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Northeastern University [Boston] (360 Huntington Ave., Boston, Massachusetts 02115 - United States)
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Rice University [Houston] (P.O. Box 1892, Houston, Texas 77251-1892 - United States)
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Affiliation as printed
Virginia Polytechnic Institute and State University [Blacksburg] (302 Whittemore Blacksburg VA 24061 - United States)
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Institució Catalana de Recerca i Estudis Avançats · Universitat de Girona
Affiliation as printed
ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies (Passeig Lluís Companys 23, 08010 Barcelona - Spain)
UdG - Universitat de Girona = University of Girona (Plaça Sant Domènec, 3 - Edifici Les Àligues - 17004 Girona - Spain)
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Affiliation as printed
Queen's University [Kingston, Canada] (99 University Ave, Kingston, ON K7L 3N6 - Canada)
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Institut Pasteur de Montevideo
Affiliation as printed
Institut Pasteur de Montevideo (Mataojo 2020, 11400 Montevideo - Uruguay)
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Italian Institute of Technology
Affiliation as printed
IIT - Italian Institute of Technology = Istituto Italiano di Tecnologia (Istituto Italiano di Tecnologia (IIT). Via Morego 30 16163 Genova, Italy - Italy)
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San Sebastián University · Fundación Ciencia and Vida
Affiliation as printed
Fundación Ciencia & Vida (Avda. del Valle Norte N° 725 Huechuraba, Santiago - Chile)
USS - Universidad San Sebastian = San Sebastian University [Santiago, Chile] (Bellavista 7, Recoleta, Santiago - Chile)
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Affiliation as printed
UMG - Università degli Studi 'Magna Graecia' di Catanzaro = University of Catanzaro (Campus Universitario 'Salvatore Venuta', Viale Europa, (88100 Catanzaro, Italie - Italy)
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Laboratoire de Chimie Théorique
Affiliation as printed
LCT - Laboratoire de chimie théorique (Tour 12-13, 4ème étage, 4 place Jussieu, Case Courrier 137, 75252 PARIS - France)
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Affiliation as printed
PAN - Polska Akademia Nauk = Polish Academy of Sciences = Académie polonaise des sciences (Pałac Kultury i Nauki, pl. Defilad 1, 00-901 Warszawa, skrytka pocztowa 24, Polska - Poland)
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University of Ljubljana · National Institute of Chemistry
Affiliation as printed
KI - National Institute of Chemistry [Llubljana] (Hajdrihova 19, 1001 Ljubljana - Slovenia)
University of Ljubljana (Kongresni trg 12, 1000 Ljubljana - Slovenia)
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Affiliation as printed
Universidade do Porto = University of Porto (Praça de Gomes Teixeira, 4099-002 Porto - Portugal)
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Affiliation as printed
UiB - University of Bergen (Universitetet i Bergen | Postboks 7800, NO-5020 Bergen - Norway)
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Affiliation as printed
UF - University of Florida [Gainesville] (Gainesville, FL 32611 - United States)
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Affiliation as printed
UCL - University College of London [London] (Gower Street, London WC1E 6BT - United Kingdom)
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Institució Catalana de Recerca i Estudis Avançats · Universitat de Barcelona
Affiliation as printed
ICREA - Institució Catalana de Recerca i Estudis Avançats = Catalan Institution for Research and Advanced Studies (Passeig Lluís Companys 23, 08010 Barcelona - Spain)
UB - Universitat de Barcelona (Gran Via de les Corts Catalanes, 585, 08007 Barcelona - Spain)
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Affiliation as printed
University of Chicago (Edward H. Levi Hall 5801 South Ellis Avenue Chicago, Illinois 60637 - United States)
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École Polytechnique Fédérale de Lausanne
Affiliation as printed
EPFL - Ecole Polytechnique Fédérale de Lausanne (CH-1015 Lausanne, Switzerland - Switzerland)
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Los Alamos National Laboratory · New Mexico Consortium
Affiliation as printed
LANL - Los Alamos National Laboratory (P.O. Box 1663 Los Alamos, NM 87545 - United States)
NMC - New Mexico Consortium (4200 W. Jemez Rd, Suite 301 Los Alamos, NM 87544 - United States)
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Affiliation as printed
NYU - New York University [New York] (70 Washington Square South, New York, NY 10012 - United States)
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