ArticleNature methods2025
The need to implement FAIR principles in biomolecular simulations.
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Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers, 1 of them a synthesis that pooled it.
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40citing papers in PubMed, 1 pooled it
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
40 citing papers in PubMed, 1 synthesis or guideline pooled it.
- (Re)defining the human chromatome: an integrated meta-analysis of localization, function, abundance, physical properties, and domain composition of chromatin proteins.Nucleic acids research · 2026Pooled it
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- From reproducibility to comparability in computational photochemistry: lessons from the PhotoChem explorer prototype.Faraday discussions · 2026Article
- ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models.Journal of molecular biology · 2026Article
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.Journal of chemical theory and computation · 2026Article
- Guidelines for Comparing Circular Dichroism Spectroscopy and Molecular Dynamics Simulations for Biomolecules.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Bayesian Modeling of Polarizable Water: Lessons for Force Field Development.Journal of chemical theory and computation · 2026Article
- An optimized contact map for GōMartini 3 enabling conformational changes in protein assemblies.Biophysical journal · 2026Article
- Advances and challenges in multiscale biomolecular simulations: artificial intelligence-driven paradigm shift.Quantitative biology (Beijing, China) · 2026Article
- Knowledge preservation in the era of big science and AI: strategies for sustainable scientific research.Nature communications · 2026Review
- PDBe-SIFTS: an open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search.bioRxiv : the preprint server for biology · 2026Article
- Management discussion of laws and regulations on human genetic resources in China: a scoping review.BMC medical ethics · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.ArXiv · 2026Article
- Influence of extracellular magnesium ions on the functional state and biophysical and structural properties of connexin36 hemichannels.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- plotXVG: Batch Generation of Publication-Quality Graphs from GROMACS Output.Journal of chemical information and modeling · 2026Article
- Glycans Modulate the Adsorption of RBD Glycoproteins on Polarizable Surfaces.Journal of chemical information and modeling · 2026Article
- From Brewing to Plastic Degradation: Uncovering the Polyurethanase Potential ofJournal of the American Chemical Society · 2026Article
- Compartment-guided assembly of large-scale molecular models with Bentopy.Protein science : a publication of the Protein Society · 2026Article
- Assessing the adoption of the FAIR principles in Italian environmental research infrastructures.Patterns (New York, N.Y.) · 2026Article
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Authors and funding
129 authors.
Rommie E AmaroDepartment of Molecular Biology, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-9275-9553
Johan ÅqvistDepartment of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Ivet BaharLaufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.ORCID http://orcid.org/0000-0001-9959-4176
Federica BattistiniDepartment of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain.
Adam BellaicheEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
Daniel BeltranInstitute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
Philip C BigginStructural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK.
Massimiliano BonomiInstitut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.ORCID http://orcid.org/0000-0002-7321-0004
Gregory R BowmanDepartment of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-2083-4892
Richard A BryceDivision of Pharmacy and Optometry, University of Manchester, Manchester, UK.
Giovanni BussiScuola Internazionale Superiore di Studi Avanzati-SISSA, Trieste, Italy.ORCID http://orcid.org/0000-0001-9216-5782
Paolo CarloniComputational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany.
David A CaseDepartment of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ, USA.
Andrea CavalliIstituto Italiano di Tecnologia, Drug Discovery and Development, Bologna, Italy.
Chia-En A ChangDepartment of Chemistry, University of California, Riverside, CA, USA.
Thomas E CheathamDepartment of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT, USA.
Margaret S CheungDepartment of Physics, University of Washington, Seattle, Washington, USA.
Christophe ChipotLIA CNRS-UIUC, UMR 7019, Université de Lorraine, Vandœuvre-lès-Nancy, France.ORCID http://orcid.org/0000-0002-9122-1698
Lillian T ChongDepartment of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
Preeti ChoudharyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
G Andres CisnerosDepartment of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA.ORCID http://orcid.org/0000-0001-6629-3430
Cecilia ClementiTheoretical and Computational Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany.
Rosana Collepardo-GuevaraMaxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
Peter CoveneyCentre for Computational Science, University College London, London, UK.ORCID http://orcid.org/0000-0002-8787-7256
Roberto CovinoInstitute of Computer Science, Goethe University Frankfurt, Frankfurt am Main, Germany.ORCID http://orcid.org/0000-0003-0884-0402
T Daniel CrawfordMolecular Sciences Software Institute, Blacksburg, VA, USA.
Matteo Dal PeraroInstitute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.ORCID http://orcid.org/0000-0002-2973-3975
Bert L de GrootComputational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.ORCID http://orcid.org/0000-0003-3570-3534
Lucie DelemotteDepartment of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.ORCID http://orcid.org/0000-0002-0828-3899
Marco De VivoLaboratory of Molecular Modelling & Drug Discovery, Istituto Italiano di Tecnologia, Genoa, Italy.
Jonathan W EssexSchool of Chemistry and Chemical Engineering, University of Southampton, Southampton, UK.ORCID http://orcid.org/0000-0003-2639-2746
Franca FraternaliInstitute of Structural and Molecular Biology, University College London, London, UK.ORCID http://orcid.org/0000-0002-3143-6574
Jiali GaoDepartment of Chemistry, University of Minnesota, Minneapolis, MN, USA.
Josep Ll GelpíDepartment of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain.ORCID http://orcid.org/0000-0002-0566-7723
Francesco L GervasioPharmaceutical Sciences, University of Geneva, Geneva, Switzerland.ORCID http://orcid.org/0000-0003-4831-5039
Fernando D González-NiloCenter for Bioinformatics and Integrative Biology (CBIB), Facultad Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.ORCID http://orcid.org/0000-0001-6857-3575
Helmut GrubmüllerDepartment of Theoretical and Computational Biophysics, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany.ORCID http://orcid.org/0000-0002-3270-3144
Marina G GuenzaDepartment of Chemistry and Biochemistry, University of Oregon, Eugene, OR, USA.ORCID http://orcid.org/0000-0002-1151-4766
Horacio V GuzmanInstitut de Ciència de Materials de Barcelona, CSIC, Barcelona, Spain.ORCID http://orcid.org/0000-0003-2564-3005
Sarah HarrisSchool of Physics and Astronomy, University of Sheffield, Sheffield, UK.
Teresa Head-GordonPitzer Theory Center and Departments of Chemistry, Bioengineering, Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-0025-8987
Rigoberto HernandezDepartment of Chemistry, Johns Hopkins University, Baltimore, MD, USA.
Adam HospitalInstitute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain. adam.hospital@irbbarcelona.org.ORCID http://orcid.org/0000-0002-8291-8071
Niu HuangNational Institute of Biological Sciences, Beijing, China.ORCID http://orcid.org/0000-0002-6912-033X
Xuhui HuangDepartment of Chemistry, Data Science Institute, University of Wisconsin-Madison, Madison, WI, USA.ORCID http://orcid.org/0000-0002-7119-9358
Gerhard HummerDepartment of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.ORCID http://orcid.org/0000-0001-7768-746X
Javier Iglesias-FernándezNBD | Nostrum Biodiscovery, Barcelona, Spain.
Jan H JensenDepartment of Chemistry, University of Copenhagen, Copenhagen, Denmark.
Shantenu JhaDepartment of Electrical and Computer Engineering, Rutgers University, New Brunswick, NJ, USA.
Wanting JiaoFerrier Research Institute, Victoria University of Wellington, Wellington, New Zealand.ORCID http://orcid.org/0000-0002-0234-7206
William L JorgensenDepartment of Chemistry, Yale University, New Haven, CT, USA.
Shina C L KamerlinDepartment of Chemistry, Lund University, Lund, Sweden.ORCID http://orcid.org/0000-0002-3190-1173
Syma KhalidStructural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-3694-5044
Charles LaughtonSchool of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK.ORCID http://orcid.org/0000-0003-4090-3960
Michael LevittDepartment of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Vittorio LimongelliEuler Institute, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), Lugano, Switzerland.
Erik LindahlDepartment of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.
Kresten Lindorff-LarsenStructural Biology and NMR Laboratory & the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.ORCID http://orcid.org/0000-0002-4750-6039
Sharon LoverdeDepartment of Chemistry, College of Staten Island, The City University of New York, New York, NY, USA.ORCID http://orcid.org/0000-0002-7643-6498
Magnus LundborgDepartment of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden.ORCID http://orcid.org/0000-0002-0873-7854
Yun L LuoCollege of Pharmacy, Western University of Health Sciences, Pomona, CA, USA.ORCID http://orcid.org/0000-0003-3581-754X
F Javier LuqueInstitute of Biomedicine, University of Barcelona, Santa Coloma de Gramanet, Spain.ORCID http://orcid.org/0000-0002-8049-3567
Charlotte I LynchStructural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0001-6619-6331
Alexander D MacKerellDepartment of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, USA.ORCID http://orcid.org/0000-0001-8287-6804
Alessandra MagistratoNational Research Council-Institute of Material Foundry at Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
Siewert J MarrinkGroningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.ORCID http://orcid.org/0000-0001-8423-5277
Hugh MartinCentre for Computational Science, University College London, London, UK.
J Andrew McCammonDepartment of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-3065-1456
Kenneth MerzLerner Research Institute Cleveland Clinic, Cleveland, OH, USA.ORCID http://orcid.org/0000-0001-9139-5893
Vicent MolinerBioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón, Spain.
Adrian J MulhollandCentre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK.ORCID http://orcid.org/0000-0003-1015-4567
Sohail MuradDepartment of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL, USA.
Athi N NaganathanDepartment of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India.ORCID http://orcid.org/0000-0002-1655-7802
Shikha NangiaDepartment of Biomedical and Chemical Engineering, Syracuse University, Syracuse, NY, USA.
Frank NoeDepartment of Physics, Freie Universität Berlin, Berlin, Germany.ORCID http://orcid.org/0000-0003-4169-9324
Agnes NoySchool of Physics, Engineering and Technology, University of York, York, UK.ORCID http://orcid.org/0000-0003-0673-8949
Julianna OláhDepartment of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary.
Megan L O'MaraAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.ORCID http://orcid.org/0000-0002-8764-1585
Mary Jo OndrechenDepartment of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.ORCID http://orcid.org/0000-0003-2456-4313
Jose N OnuchicDepartment of Chemistry, Rice University, Houston, TX, USA.ORCID http://orcid.org/0000-0002-9448-0388
Alexey OnufrievDepartment of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
Sílvia OsunaInstitut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Girona, Spain.
Giulia PalermoDepartment of Chemistry, University of California, Riverside, CA, USA.
Anna R PanchenkoDepartment of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, Ontario, Canada.
Sergio PantanoBiomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo, Uruguay.
Carol ParishDepartment of Chemistry, Gottwald Center for the Sciences, University of Richmond, Richmond, VA, USA.
Michele ParrinelloAtomistic Simulations, Italian Institute of Technology, Genova, Italy.
Alberto PerezDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.ORCID http://orcid.org/0000-0002-5054-5338
Tomas Perez-AcleComputational Biology Lab, Fundación Ciencia & Vida, Santiago, Chile.
Juan R PerillaDepartment of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.ORCID http://orcid.org/0000-0003-1171-6816
B Montgomery PettittUniversity of Texas Medical Branch, Galveston, TX, USA.
Adriana PietropaoloDipartimento di Scienze della Salute, Università di Catanzaro, Catanzaro, Italy.
Jean-Philip PiquemalLaboratory of Theoretical Chemistry, Department of Chemistry, Sorbonne University, Paris, France.ORCID http://orcid.org/0000-0001-6615-9426
Adolfo B PomaBiosystems and Soft Matter Division, Institute of Fundamental Technological Research, Polish Academy of Sciences, Warsaw, Poland.ORCID http://orcid.org/0000-0002-8875-3220
Matej PraprotnikLaboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia.ORCID http://orcid.org/0000-0003-0825-1659
Maria J RamosDepartment of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal.
Pengyu RenDepartment of Biomedical Engineering, The University of Texas at Austin, Austin, TX, USA.
Nathalie ReuterDepartment of Chemistry, University of Bergen, Bergen, Norway.ORCID http://orcid.org/0000-0002-3649-7675
Adrian RoitbergDepartment of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA.
Edina RostaDepartment of Physics and Astronomy, University College London, London, UK.
Carme RoviraCatalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.ORCID http://orcid.org/0000-0003-1477-5010
Benoit RouxDepartment of Chemistry, University of Chicago, Chicago, IL, USA.ORCID http://orcid.org/0000-0002-5254-2712
Ursula RothlisbergerLaboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.ORCID http://orcid.org/0000-0002-1704-8591
Karissa Y SanbonmatsuTheoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA.ORCID http://orcid.org/0000-0002-7965-7392
Tamar SchlickDepartment of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, NY, USA.
Alexey K ShaytanDepartment of Biology, Lomonosov Moscow State University, Moscow, Russia.
Carlos SimmerlingLaufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.ORCID http://orcid.org/0000-0002-7252-4730
Jeremy C SmithBiosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, USA.ORCID http://orcid.org/0000-0002-2978-3227
Yuji SugitaComputational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Japan.ORCID http://orcid.org/0000-0001-9738-9216
Katarzyna ŚwiderekBioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I, Castellón, Spain.ORCID http://orcid.org/0000-0002-7528-1551
Makoto TaijiLaboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
Peng TaoDepartment of Chemistry, O'Donnell Data Science and Research Computing Institute, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, USA.ORCID http://orcid.org/0000-0002-2488-0239
D Peter TielemanDepartment of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada.ORCID http://orcid.org/0000-0001-5507-0688
Irina G TikhonovaSchool of Pharmacy, Queen's University Belfast, Belfast, UK.ORCID http://orcid.org/0000-0002-6228-9431
Julian Tirado-RivesDepartment of Chemistry, Yale University, New Haven, CT, USA.ORCID http://orcid.org/0000-0001-7330-189X
Iñaki TuñónDepartamento de Química Física, Universidad de Valencia, Burjassot, Spain.
Marc W van der KampSchool of Biochemistry, University of Bristol, Bristol, UK.
David van der SpoelDepartment of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.ORCID http://orcid.org/0000-0002-7659-8526
Sameer VelankarEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.ORCID http://orcid.org/0000-0002-8439-5964
Gregory A VothDepartment of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL, USA.
Rebecca WadeMolecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.
Ariel WarshelDepartment of Chemistry, University of Southern California, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0001-7971-5401
Valerie Vaissier WelbornDepartment of Chemistry, Virginia Tech, Blacksburg, VA, USA.
Stacey D WetmoreDepartment of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.ORCID http://orcid.org/0000-0002-5801-3942
Travis J WheelerR. Ken Coit College of Pharmacy, University of Arizona, Tucson, Arizona, USA.
Chung F WongDepartment of Chemistry and Biochemistry, University of Missouri-St. Louis, St. Louis, MO, USA.
Lee-Wei YangInstitute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan.ORCID http://orcid.org/0000-0002-3971-6386
Martin ZachariasPhysics Department, Technical University of Munich, Garching, Germany.ORCID http://orcid.org/0000-0001-5163-2663
Modesto OrozcoDepartment of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain. modesto.orozco@irbbarcelona.org.ORCID http://orcid.org/0000-0002-8608-3278
Funding
Emergent Properties of Complex Systems: From Atoms to Macromolecules; from Humans to SocietiesR35GM122543 · NIGMS · STANFORD UNIVERSITY · PI MICHAEL LEVITT · 2017 to 2026
$5.1MModeling Transition Metal Ion Binding to ProteinsR01GM130641 · NIGMS · MICHIGAN STATE UNIVERSITY · PI KENNETH M. MERZ · 2019 to 2026
$2.5MElucidating the dynamical and structural molecular factors at the origin of non-enzymatic protein-protein and protein-DNA cross-linksR35GM150409 · NIGMS · VIRGINIA POLYTECHNIC INST AND ST UNIV · PI Valerie Vaissier Welborn · 2023 to 2026
$1.5MUnderstanding and controlling protein energy landscapes by combining simulations and experimentsR35GM152085 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI Gregory Bowman · 2024 to 2026
$1.2MComputational Methods to Characterize Structure and Dynamics of the Nucleosome Core ParticleR15GM146228 · NIGMS · COLLEGE OF STATEN ISLAND · PI LOVERDE, SHARON MARIE · 2022 to 2023
$586kEuropean Commission (EC) 101094651NIGMS NIH HHS R01 GM130641NIGMS NIH HHS R15 GM146228NIGMS NIH HHS R35 GM122543NIGMS NIH HHS R35 GM150409NIGMS NIH HHS R35 GM152085
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