Supporting Papers

List and brief description of papers supporting the research and data presented on this website:

This website is based on the following work:

  • Large-scale analysis publication: Gradations in protein dynamics captured by experimental NMR are not well represented by AlphaFold2 models and other computational metrics - J. Gavalda-Garcia, B. Dixit, A. Diaz, A. Ghysels, & W. Vranken (Preprint). Please cite this paper if you refer to this website.
  • Constava publication: Data-driven probabilistic definition of the low energy conformational states of protein residues - J. Gavalda-Garcia, D. Bickel, J. Roca-Martinez, D. Raimondi, G. Orlando & W. Vranken (Publication).

Download data

The data presented in this website can be downloaded from its Zenodo archive. This contains the complete data frames for each data set and the AlphaFold2 & AlphaFold3 structures for the S2 and Constava data sets. The AlphaFold structures for the S2RCI dataset can be downloaded from AlphaFold's protein structure database by providing a list with the protein's Uniprot accession identifiers to AlphaFetcher.

How to Use This Site

You can search for proteins in two different ways:

  • Exploring Entries: Start by visiting the Entries List page to see all available proteins. Click on any entry to view detailed information.
  • Searching for Data: Use the search bar on the Home Page to find specific entries.

Each entry page contains tabs with diverse information:

  • Overview: Protein basic information, external databases identifiers, and entry creation and update timestamps.
  • Interactive analysis: 1D-3D interactive visualisation of the AlphaFold's predicted protein structure model with protein biophysics metrics. This visualisation is based on the RCSB-Saguaro viewer.
  • Plots: Basic plots of pLDDT and protein biophysics metrics.
  • Data: Tables containing focused data, relevant to the type of information available for a protein.