ArticleThe Journal of chemical physics2025
PLUMED Tutorials: A collaborative, community-driven learning ecosystem.
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Article in The Journal of chemical physics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19citing papers in PubMed
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Who cites it
19 citing papers in PubMed.
- Structural dynamics and pH-regulated membrane binding of the TRAF2-NC trimer.Protein science : a publication of the Protein Society · 2026Article
- Integrating NMR and contact-response analysis reveals the allosteric network driving domain closure in Enzyme I.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Stepping Up Enhanced Rate Calculations with EATR-Flooding.Journal of chemical theory and computation · 2026Article
- Why Do PETases Struggle with Crystalline PET? Catalytic Ensemble Sampling Reveals Molecular Bottlenecks.The journal of physical chemistry letters · 2026Article
- A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies.The journal of physical chemistry letters · 2026Article
- Making PLUMED Fly: A Tutorial on Optimizing Performance.The journal of physical chemistry. B · 2026Article
- The seeds of the future are in the present: A blind exploration of metastable states.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies.Nucleic acids research · 2026Article
- Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications.Chemical reviews · 2026Review
- Enhanced Sampling for Efficient Learning of Coarse-Grained Machine Learning Potentials.Journal of chemical theory and computation · 2026Article
- Tutorial on quantifying and sampling biomolecular ensembles with ShapeGMM.The Journal of chemical physics · 2025Article
- Destabilization of Helix III Initiates Early Serum Amyloid A Misfolding by Exposing Its Amyloidogenic Core.The journal of physical chemistry letters · 2025Article
- Using Time Dependent Rate Analysis to Evaluate the Quality of Machine Learned Reaction Coordinates for Biasing and Computing Kinetics.The journal of physical chemistry. B · 2025Article
- The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables.The journal of physical chemistry letters · 2025Article
- Enhanced Sampling and Tailored Collective Variables Yield Reproducible Free Energy Landscapes of Beta-1 Adrenergic Receptor Activation.Journal of chemical theory and computation · 2025Article
- NeuralTSNE: A Python Package for the Dimensionality Reduction of Molecular Dynamics Data Using Neural Networks.Journal of chemical information and modeling · 2025Article
- A direct computational assessment of vinculin-actin unbinding kinetics reveals catch-bonding behavior.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Characterizing RNA Oligomers Using Stochastic Titration Constant-pH Metadynamics Simulations.Journal of chemical information and modeling · 2025Article
- AlphaFold prediction of structural ensembles of disordered proteins.Nature communications · 2025Article
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Authors and funding
63 authors.
Gareth A TribelloCentre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast, Belfast, United Kingdom.ORCID 0000-0002-4763-9317
Massimiliano BonomiInstitut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.ORCID 0000-0002-7321-0004
Giovanni BussiScuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.ORCID 0000-0001-9216-5782
Carlo CamilloniDepartment of Biosciences, University of Milano, Milano, Italy.ORCID 0000-0002-9923-8590
Blake I ArmstrongSchool of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.ORCID 0000-0002-9237-4012
Andrea ArsiccioCoriolis Pharma, Fraunhoferstrasse 18b, 82152 Martinsried, Germany.ORCID 0000-0003-3809-4957
Simone AureliSchool of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, Switzerland.ORCID 0000-0002-4938-8603
Federico BallabioCentre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast, Belfast, United Kingdom.ORCID 0000-0001-5702-3674
Mattia BernettiCentre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast, Belfast, United Kingdom.ORCID 0000-0002-4373-9310
Luigi BonatiAtomistic Simulations, Italian Institute of Technology, Genova, Italy.ORCID 0000-0002-9118-6239
Samuel G H BrookesCentre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast, Belfast, United Kingdom.ORCID 0000-0003-2821-7255
Z Faidon BrotzakisCentre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast, Belfast, United Kingdom.ORCID 0000-0001-7024-1430
Riccardo CapelliDepartment of Biosciences, University of Milano, Milano, Italy.ORCID 0000-0001-9522-3132
Michele CeriottiLaboratory of Computational Science and Modeling, Institut des Matériaux, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.ORCID 0000-0003-2571-2832
Kam-Tung ChanDepartment of Chemistry, University of California, Davis, Davis, California 95616, USA.ORCID 0000-0001-7811-8314
Pilar CossioCentre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast, Belfast, United Kingdom.ORCID 0000-0002-5404-9948
Siva DasettyPritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA.ORCID 0000-0002-1666-7980
Davide DonadioDepartment of Chemistry, University of California, Davis, Davis, California 95616, USA.ORCID 0000-0002-2150-4182
Bernd EnsingInstitut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.ORCID 0000-0002-4913-3571
Andrew L FergusonInstitut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.ORCID 0000-0002-8829-9726
Guillaume FrauxCentre for Quantum Materials and Technologies, School of Mathematics and Physics, Queen's University Belfast, Belfast, United Kingdom.ORCID 0000-0003-4824-6512
Julian D GaleSchool of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.ORCID 0000-0001-9587-9457
Francesco Luigi GervasioInstitut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.ORCID 0000-0003-4831-5039
Toni GiorginoNational Research Council of Italy, Biophysics Institute (CNR-IBF), Via Celoria 26, Milan 20133, Italy.ORCID 0000-0001-6449-0596
Nicholas S M HerringerDepartment of Chemistry, University of Chicago, Chicago, Illinois 60637, USA.ORCID 0009-0001-5039-7304
Glen M HockyDepartment of Chemistry, Simons Center for Computational Physical Chemistry, New York University, New York, New York 10012, USA.ORCID 0000-0002-5637-0698
Samuel E HoffInstitut Pasteur, Université Paris Cité, CNRS UMR 3528, Computational Structural Biology Unit, Paris, France.ORCID 0009-0006-8901-221X
Michele InvernizziPeptone Ltd., The Connolly Works 41-43, Chalton Street, London NW1 1JD, United Kingdom.ORCID 0000-0002-3328-6557
Olivier Languin-CattoënScuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.ORCID 0000-0002-0486-9841
Vanessa LeoneDepartment of Biophysics and Data Science Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226-3548, USA.
Vittorio LimongelliEuler Institute, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), via G. Buffi 13, CH-6900 Lugano, Switzerland.ORCID 0000-0002-4861-1199
Olga Lopez-AcevedoBiophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA, 050010 Medellin, Colombia.ORCID 0000-0003-4489-6841
Fabrizio MarinelliDepartment of Biophysics and Data Science Institute, Medical College of Wisconsin, Milwaukee, Wisconsin 53226-3548, USA.ORCID 0000-0003-0044-6718
Pedro Febrer MartinezSchool of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, Switzerland.ORCID 0009-0007-0627-1871
Matteo MasettiDepartment of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy.ORCID 0000-0002-3757-7802
Shams MehdiDepartment of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA.ORCID 0000-0002-4078-7501
Angelos MichaelidesYusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom.ORCID 0000-0002-9169-169X
Mhd Hussein MurtadaCentre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.ORCID 0000-0003-3402-8864
Michele ParrinelloAtomistic Simulations, Italian Institute of Technology, Genova, Italy.ORCID 0000-0001-6550-3272
Pablo M PiaggiCIC nanoGUNE BRTA, Tolosa Hiribidea 76, 20018 Donostia-San Sebastián, Spain and Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain.ORCID 0000-0003-0225-0081
Adriana PietropaoloDipartimento di Scienze della Salute, Università Magna Graecia di Catanzaro, Viale Europa, 88100 Catanzaro, Italy.ORCID 0000-0003-0955-2058
Fabio PietrucciInstitut de Minéralogie, de Physique des Matériaux et de Cosmochimie, UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, Paris 75005, France.ORCID 0000-0002-4892-2667
Silvio PipoloUCCS Unité de Catalyse et Chimie du Solide, Université de Lille, Université d'Artois UMR 8181, F-59000 Lille, France.ORCID 0000-0003-2828-073X
Claire PritchardPASTEUR, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France.ORCID 0009-0008-5457-1841
Paolo RaiteriSchool of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.ORCID 0000-0003-0692-0505
Stefano RanioloEuler Institute, Faculty of Biomedical Sciences, Università della Svizzera italiana (USI), via G. Buffi 13, CH-6900 Lugano, Switzerland.ORCID 0000-0003-4835-8696
Daniele RapettiScuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.ORCID 0000-0002-7193-5220
Valerio RizziSchool of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, Switzerland.ORCID 0000-0001-5126-8996
Jakub RydzewskiFaculty of Physics, Astronomy and Informatics, Institute of Physics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland.ORCID 0000-0003-4325-4177
Matteo SalvalaglioThomas Young Centre and Department of Chemical Engineering, University College London, London WC1E 7JE, United Kingdom.ORCID 0000-0003-3371-2090
Christoph SchranCavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, United Kingdom.ORCID 0000-0003-4595-5073
Aniruddha SealDepartment of Chemistry, University of Chicago, Chicago, Illinois 60637, USA.ORCID 0000-0002-5710-5378
Armin Shayesteh ZadehPritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA.ORCID 0000-0002-9989-6710
Tomás F D SilvaScuola Internazionale Superiore di Studi Avanzati (SISSA), Via Bonomea 265, 34136 Trieste, Italy.ORCID 0000-0003-4608-2673
Vojtěch SpiwokUniversity of Chemistry and Technology, Technická 5, CZ-166 28 Praha 6, Czech Republic.ORCID 0000-0001-8108-2033
Guillaume StirnemannPASTEUR, Département de chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 24 rue Lhomond, 75005 Paris, France.ORCID 0000-0002-5631-5699
Daniel SucerquiaHeidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.ORCID 0000-0003-1287-0153
Pratyush TiwaryDepartment of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA.ORCID 0000-0002-2412-6922
Omar ValssonDepartment of Chemistry, University of North Texas, Denton, Texas 76201, USA.ORCID 0000-0001-7971-4767
Michele VendruscoloCentre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.ORCID 0000-0002-3616-1610
Gregory A VothDepartment of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, USA.ORCID 0000-0002-3267-6748
Andrew D WhiteDepartment of Chemical Engineering, University of Rochester, Rochester, New York 14627, USA.ORCID 0000-0002-6647-3965
Jiangbo WuDepartment of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, University of Chicago, Chicago, Illinois 60637, USA.ORCID 0009-0002-7716-6079
Funding
Harnessing simulations to uncover molecular mechanisms of mechanosensingR35GM138312 · NIGMS · NEW YORK UNIVERSITY · PI Glen Hocky · 2020 to 2026
$3.0MNIGMS NIH HHS R35 GM138312
Abstract
In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents several challenges. Common methods like direct knowledge transfer and in-person workshops are limited in reach and comprehensiveness. Furthermore, while the COVID-19 pandemic highlighted the benefits of online training, traditional online tutorials can quickly become outdated and may not cover all the software's functionalities. To address these issues, here we introduce "PLUMED Tutorials," a collaborative model for developing, sharing, and updating online tutorials. This initiative utilizes repository management and continuous integration to ensure compatibility with software updates. Moreover, the tutorials are interconnected to form a structured learning path and are enriched with automatic annotations to provide broader context. This paper illustrates the development, features, and advantages of PLUMED Tutorials, aiming to foster an open community for creating and sharing educational resources.
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