Data collection & curation

To collect amyloid-related databases, we searched PubMed, Google and Google Scholar databases using queries such as “amyloid database”, “IDP database”, “prion database, etc.

We manually curated all information for databases featured in a Amyloid-related database list tab. To do that we carefully analysed publications and/or websites describing given database looking for the following information:

  • link to the web server (integrated into Database name column),
  • what is their focus, amyloids, prions, IDPs, interactions (Focus column)
  • what kind of data do they store, experimental, predictions or both (Type of data column)
  • do they store only amyloids (Only amyloids column)
  • do they include experimental conditions (Includes experimental conditions column)
  • usability of data creating generalized models (Usability column),
  • what kind of structural information is gathered (*Includes structural information** column),
  • do they highlight proteins APRs (Identifies APRs column),
  • current status of database (Current status),
  • date of last update or publication date (Published or last update column),
  • external sources of proteins/peptides in database (we didn’t mention own discoveries) and links to and other sources that are integrated into the database (Data sources and links to other db column),
  • link to publication (DOI column)

Then, we checked if the links to the databases provided in the articles function correctly. Otherwise, we tried to find them either through a search engine or by contacting the database developers.

The Updates tab indicates latest changes in the list.

Updates

05/11/2024 - article online, added citation

30/09/2024 - change status of ZipperDB to non-functional instead of non-active

08/08/2024 - minor name corrections made | No status changes in inactive amyloid databases | Server instability reported for AmyLoad

17/07/2024 - first release

About and citation

The database was developed by BioGenies team. If you want to get to know us and our projects visit our webpage BioGenies.

This website accompanies our publication:

Iglesias V, Chilimoniuk J, Pintado-Grima C, Bárcenas O, Ventura S, Burdukiewicz M (2024). “Aggregating Amyloid Resources: A Comprehensive Review of Databases on Amyloid-like Aggregation.” Computational and Structural Biotechnology Journal. ISSN 2001-0370, doi:10.1016/j.csbj.2024.10.047, https://doi.org/10.1016/j.csbj.2024.10.047, <2024-11-05>

This project was supported by the National Science Centre Poland, SONATA 19 grant [2023/51/D/NZ7/02847].

National Science Centre Poland

Open access was funded by Medical University of Białystok, [B.SUB.24.592].

Medical University of Bialystok