| URL: | https://proteinensemble.org |
| Full name: | Protein Ensemble Database |
| Description: | The goal of the PED project is to provide a platform for the IDP community where ensembles and their corresponding primary data can be stored and used as benchmarking datasets to facilitate the development of new ensemble calculation methods. |
| Year founded: | 2021 |
| Last update: | 2020 |
| Version: | 4.0 |
| Accessibility: |
Accessible
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| Country/Region: | Italy |
| Data type: | |
| Data object: |
NA
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| Database category: | |
| Major species: |
NA
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| Keywords: |
| University/Institution: | University of Padua |
| Address: | University of Padua, Department of Biomedical Sciences Viale G. Colombo 3 35131 Padua, Italy +39 049 827 6269 |
| City: | |
| Province/State: | |
| Country/Region: | Italy |
| Contact name (PI/Team): | Damiano Piovesan |
| Contact email (PI/Helpdesk): | ped@ngp-net.bio.unipd.it |
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PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins. [PMID: 37904608]
The Protein Ensemble Database (PED) (URL: https://proteinensemble.org) is the primary resource for depositing structural ensembles of intrinsically disordered proteins. This updated version of PED reflects advancements in the field, denoting a continual expansion with a total of 461 entries and 538 ensembles, including those generated without explicit experimental data through novel machine learning (ML) techniques. With this significant increment in the number of ensembles, a few yet-unprecedented new entries entered the database, including those also determined or refined by electron paramagnetic resonance or circular dichroism data. In addition, PED was enriched with several new features, including a novel deposition service, improved user interface, new database cross-referencing options and integration with the 3D-Beacons network-all representing efforts to improve the FAIRness of the database. Foreseeably, PED will keep growing in size and expanding with new types of ensembles generated by accurate and fast ML-based generative models and coarse-grained simulations. Therefore, among future efforts, priority will be given to further develop the database to be compatible with ensembles modeled at a coarse-grained level. |
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PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins. [PMID: 33305318]
The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs. |