Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins
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arXiv
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| Auteurs principaux: | , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Preprint |
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2025
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| _version_ | 1866911102698258432 |
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| author | Ghafouri, Hamidreza Kadeřávek, Pavel Melo, Ana M Aspromonte, Maria Cristina Bernadó, Pau Cortes, Juan Dosztányi, Zsuzsanna Erdos, Gabor Feig, Michael Janson, Giacomo Lindorff-Larsen, Kresten Mulder, Frans A. A. Nagy, Peter Pestell, Richard Piovesan, Damiano Schiavina, Marco Schuler, Benjamin Sibille, Nathalie Tesei, Giulio Tompa, Peter Vendruscolo, Michele Vondrasek, Jiri Vranken, Wim Zidek, Lukas Tosatto, Silvio C. E. Monzon, Alexander Miguel |
| author_facet | Ghafouri, Hamidreza Kadeřávek, Pavel Melo, Ana M Aspromonte, Maria Cristina Bernadó, Pau Cortes, Juan Dosztányi, Zsuzsanna Erdos, Gabor Feig, Michael Janson, Giacomo Lindorff-Larsen, Kresten Mulder, Frans A. A. Nagy, Peter Pestell, Richard Piovesan, Damiano Schiavina, Marco Schuler, Benjamin Sibille, Nathalie Tesei, Giulio Tompa, Peter Vendruscolo, Michele Vondrasek, Jiri Vranken, Wim Zidek, Lukas Tosatto, Silvio C. E. Monzon, Alexander Miguel |
| contents | Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address this problem by advocating a unified framework for determining conformational ensembles of disordered proteins. Our aim is to integrate state-of-the-art experimental techniques with advanced computational methods, including knowledge-based sampling, enhanced molecular dynamics, and machine learning models. The modular framework comprises three interconnected components: experimental data acquisition, computational ensemble generation, and validation. The systematic development of this framework will ensure the accurate and reproducible determination of conformational ensembles of disordered proteins. We highlight the open challenges necessary to achieve this goal, including force field accuracy, efficient sampling, and environmental dependency, advocating for collaborative benchmarking and standardized protocols. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2504_03590 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins Ghafouri, Hamidreza Kadeřávek, Pavel Melo, Ana M Aspromonte, Maria Cristina Bernadó, Pau Cortes, Juan Dosztányi, Zsuzsanna Erdos, Gabor Feig, Michael Janson, Giacomo Lindorff-Larsen, Kresten Mulder, Frans A. A. Nagy, Peter Pestell, Richard Piovesan, Damiano Schiavina, Marco Schuler, Benjamin Sibille, Nathalie Tesei, Giulio Tompa, Peter Vendruscolo, Michele Vondrasek, Jiri Vranken, Wim Zidek, Lukas Tosatto, Silvio C. E. Monzon, Alexander Miguel Biomolecules Quantitative Methods Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address this problem by advocating a unified framework for determining conformational ensembles of disordered proteins. Our aim is to integrate state-of-the-art experimental techniques with advanced computational methods, including knowledge-based sampling, enhanced molecular dynamics, and machine learning models. The modular framework comprises three interconnected components: experimental data acquisition, computational ensemble generation, and validation. The systematic development of this framework will ensure the accurate and reproducible determination of conformational ensembles of disordered proteins. We highlight the open challenges necessary to achieve this goal, including force field accuracy, efficient sampling, and environmental dependency, advocating for collaborative benchmarking and standardized protocols. |
| title | Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins |
| topic | Biomolecules Quantitative Methods |
| url | https://arxiv.org/abs/2504.03590 |