Promoting transparency and reproducibility in enhanced molecular simulations
Autor: | B. Pavel, L. Vittorio, C. Michele, F. Marta, W. Andrew, G. Federico, V. Michele, Š. Jiří, Davide Provasi, M. Layla, K. Evgeny, S. Matteo, V. Omar, Riccardo Capelli, M. Carla, David W.H. Swenson, Kim E. Jelfs, G. Piero, D. Davide, M. Angelos, P. Jim, Gareth A. Tribello, M. Fabrizio, C. Francesco, P. Michele, E. Bernd, Cristina Paissoni, M. Matteo, F. Haohao, L. Kresten, P. Pablo, T. Pratyush, L. Alessandro, Marco De La Pierre, B. Mattia, J. Alexander, M. Tetsuya, B. Sandro, Andrew L. Ferguson, Gabriella T. Heller, Francesco Luigi Gervasio, B. Davide, R. Paolo, D. Viktor, Massimiliano Bonomi, I. Michele, Peter G. Bolhuis, P. GiovanniMaria, Carlo Camilloni, C. Andrea, P. Elena, S. Vojtěch, James S. Fraser, L. Thomas, C. Haochuan, C. Paolo, N. Marco, B. Alessandro, P. Fabio, B. Giovanni, I. Marcella, G. Alejandro, C. Wei, Glen M. Hocky, G. Toni, P. Adriana, Gabriele C. Sosso, Q. David, P. Silvio, Gregory A. Voth, M. Ralf, R. Stefano, D. Sandip, R. Jakub |
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Přispěvatelé: | The Royal Society, Département de Biologie structurale et Chimie - Department of Structural Biology and Chemistry, Institut Pasteur [Paris] (IP), Bioinformatique structurale - Structural Bioinformatics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Scuola Internazionale Superiore di Studi Avanzati / International School for Advanced Studies (SISSA / ISAS), Università degli Studi di Milano = University of Milan (UNIMI), Queen's University [Belfast] (QUB), Centre de Biochimie Structurale [Montpellier] (CBS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Unité de Catalyse et Chimie du Solide - UMR 8181 (UCCS), Université d'Artois (UA)-Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre Blaise Pascal (CBP), École normale supérieure de Lyon (ENS de Lyon), University of Rochester [USA], Bonomi, M., Bussi, G., Camilloni, C., Tribello, G. A., Banas, P., Barducci, A., Bernetti, M., Bolhuis, P. G., Bottaro, S., Branduardi, D., Capelli, R., Carloni, P., Ceriotti, M., Cesari, A., Chen, H., Chen, W., Colizzi, F., De, S., De La Pierre, M., Donadio, D., Drobot, V., Ensing, B., Ferguson, A. L., Filizola, M., Fraser, J. S., Fu, H., Gasparotto, P., Gervasio, F. L., Giberti, F., Gil-Ley, A., Giorgino, T., Heller, G. T., Hocky, G. M., Iannuzzi, M., Invernizzi, M., Jelfs, K. E., Jussupow, A., Kirilin, E., Laio, A., Limongelli, V., Lindorff-Larsen, K., Lohr, T., Marinelli, F., Martin-Samos, L., Masetti, M., Meyer, R., Michaelides, A., Molteni, C., Morishita, T., Nava, M., Paissoni, C., Papaleo, E., Parrinello, M., Pfaendtner, J., Piaggi, P., Piccini, G. M., Pietropaolo, A., Pietrucci, F., Pipolo, S., Provasi, D., Quigley, D., Raiteri, P., Raniolo, S., Rydzewski, J., Salvalaglio, M., Sosso, G. C., Spiwok, V., Sponer, J., Swenson, D. W. H., Tiwary, P., Valsson, O., Vendruscolo, M., Voth, G. A., White, A., Institut Pasteur [Paris], Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Milano [Milano] (UNIMI), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centrale Lille Institut (CLIL)-Université d'Artois (UA)-Centrale Lille-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Lille, École normale supérieure - Lyon (ENS Lyon), Simulation of Biomolecular Systems (HIMS, FNWI), Molecular Simulations (HIMS, FNWI), Massimiliano Bonomi, Giovanni Bussi, Carlo Camilloni, Gareth A. Tribello, Pavel Banáš, Alessandro Barducci, Mattia Bernetti, Peter G. Bolhuis, Sandro Bottaro, Davide Branduardi, Riccardo Capelli, Paolo Carloni, Michele Ceriotti, Andrea Cesari, Haochuan Chen, Wei Chen, Francesco Colizzi, Sandip De, Marco De La Pierre, Davide Donadio, Viktor Drobot, Bernd Ensing, Andrew L. Ferguson, Marta Filizola, James S. Fraser, Haohao Fu, Piero Gasparotto, Francesco Luigi Gervasio, Federico Giberti, Alejandro Gil-Ley, Toni Giorgino, Gabriella T. Heller, Glen M. Hocky, Marcella Iannuzzi, Michele Invernizzi, Kim E. Jelfs, Alexander Jussupow, Evgeny Kirilin, Alessandro Laio, Vittorio Limongelli, Kresten Lindorff-Larsen, Thomas Löhr, Fabrizio Marinelli, Layla Martin-Samos, Matteo Masetti, Ralf Meyer, Angelos Michaelides, Carla Molteni, Tetsuya Morishita, Marco Nava, Cristina Paissoni, Elena Papaleo, Michele Parrinello, Jim Pfaendtner, Pablo Piaggi, GiovanniMaria Piccini, Adriana Pietropaolo, Fabio Pietrucci, Silvio Pipolo, Davide Provasi, David Quigley, Paolo Raiteri, Stefano Raniolo, Jakub Rydzewski, Matteo Salvalaglio, Gabriele Cesare Sosso, Vojtěch Spiwok, Jiří Šponer, David W. H. Swenson, Pratyush Tiwary, Omar Valsson, Michele Vendruscolo, Gregory A. Voth & Andrew White |
Rok vydání: | 2019 |
Předmět: |
Models
Molecular DYNAMICS enhanced-sampling free-energy calculations molecular dynamics simulations transparency reproducibility dissemination Biochemistry & Molecular Biology Computer science Molecular Conformation Molecular Dynamics Simulation Biochemistry Biochemical Research Methods Settore FIS/03 - Fisica della Materia 03 medical and health sciences 10 Technology Humans ddc:610 reproducibility Molecular Biology ComputingMilieux_MISCELLANEOUS 11 Medical and Health Sciences 030304 developmental biology 0303 health sciences Reproducibility Science & Technology PLUMED consortium Reproducibility of Results Cell Biology 06 Biological Sciences simulation [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] Transparency (graphic) Systems engineering Life Sciences & Biomedicine Software Biotechnology Developmental Biology |
Zdroj: | Nature Methods Nature Methods, 2019, 16 (8), pp.670-673. ⟨10.1038/s41592-019-0506-8⟩ The PLUMED consortium 2019, ' Promoting transparency and reproducibility in enhanced molecular simulations ', Nature Methods, vol. 16, no. 8, pp. 670-673 . https://doi.org/10.1038/s41592-019-0506-8 Nature methods 16(8), 670-673 (2019). doi:10.1038/s41592-019-0506-8 Nature Methods, Nature Publishing Group, 2019, 16 (8), pp.670-673. ⟨10.1038/s41592-019-0506-8⟩ Bonomi, M, Bussi, G, Camilloni, C, Tribello, G A, Banas, P, Barducci, A, Bernetti, M, Bolhuis, P G, Bottaro, S, Branduardi, D, Capelli, R, Carloni, P, Ceriotti, M, Cesari, A, Chen, H, Chen, W, Colizzi, F, De, S, De La Pierre, M, Donadio, D, Drobot, V, Ensing, B, Ferguson, A L, Filizola, M, Fraser, J S, Fu, H, Gasparotto, P, Gervasio, F L, Giberti, F, Gil-Ley, A, Giorgino, T, Heller, G T, Hocky, G M, Iannuzzi, M, Invernizzi, M, Jelfs, K E, Jussupow, A, Kirilin, E, Laio, A, Limongelli, V, Lindorff-Larsen, K, Lohr, T, Marinelli, F, Martin-Samos, L, Masetti, M, Meyer, R, Michaelides, A, Molteni, C, Morishita, T, Nava, M, Paissoni, C, Papaleo, E, Parrinello, M, Pfaendtner, J, Piaggi, P, Piccini, G, Pietropaolo, A, Pietrucci, F, Pipolo, S, Provasi, D, Quigley, D, Raiteri, P, Raniolo, S, Rydzewski, J, Salvalaglio, M, Sosso, G C, Spiwok, V, Sponer, J, Swenson, D W H, Tiwary, P, Valsson, O, Vendruscolo, M, Voth, G A & White, A 2019, ' Promoting transparency and reproducibility in enhanced molecular simulations ', Nature Methods, vol. 16, no. 8, pp. 670-673 . https://doi.org/10.1038/s41592-019-0506-8 Nature Methods, 16(8), 670-673. Nature Publishing Group Nature methods (Online) 16 (2019): 670. doi:10.1038/s41592-019-0506-8 info:cnr-pdr/source/autori:Massimiliano Bonomi, Giovanni Bussi, Carlo Camilloni, Gareth A. Tribello, Pavel Baná?, Alessandro Barducci, Mattia Bernetti, Peter G. Bolhuis, Sandro Bottaro, Davide Branduardi, Riccardo Capelli, Paolo Carloni, Michele Ceriotti, Andrea Cesari, Haochuan Chen, Wei Chen, Francesco Colizzi, Sandip De, Marco De La Pierre, Davide Donadio, Viktor Drobot, Bernd Ensing, Andrew L. Ferguson, Marta Filizola, James S. Fraser, Haohao Fu, Piero Gasparotto, Francesco Luigi Gervasio, Federico Giberti, Alejandro Gil-Ley, Toni Giorgino, Gabriella T. Heller, Glen M. Hocky, Marcella Iannuzzi, Michele Invernizzi, Kim E. Jelfs, Alexander Jussupow, Evgeny Kirilin, Alessandro Laio, Vittorio Limongelli, Kresten Lindorff-Larsen, Thomas Löhr, Fabrizio Marinelli, Layla Martin-Samos, Matteo Masetti, Ralf Meyer, Angelos Michaelides, Carla Molteni, Tetsuya Morishita, Marco Nava, Cristina Paissoni, Elena Papaleo, Michele Parrinello, Jim Pfaendtner, Pablo Piaggi, GiovanniMaria Piccini, Adriana Pietropaolo, Fabio Pietrucci, Silvio Pipolo, Davide Provasi, David Quigley, Paolo Raiteri, Stefano Raniolo, Jakub Rydzewski, Matteo Salvalaglio, Gabriele Cesare Sosso, Vojt?ch Spiwok, Ji?í ?poner, David W. H. Swenson, Pratyush Tiwary, Omar Valsson, Michele Vendruscolo, Gregory A. Voth, Andrew White/titolo:Promoting transparency and reproducibility in enhanced molecular simulations/doi:10.1038%2Fs41592-019-0506-8/rivista:Nature methods (Online)/anno:2019/pagina_da:670/pagina_a:/intervallo_pagine:670/volume:16 |
ISSN: | 1548-7091 1548-7105 |
Popis: | The PLUMED consortium unifies developers and contributors to PLUMED, an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations. Here, we outline our efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations. |
Databáze: | OpenAIRE |
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