Changelog

0.8.0

9 March, 2019
  • Added very basic structure prediction for E2 and H3 sites.
  • Fixed page loading wait bug.

0.7.1

18 February, 2019
  • Fixed BLAST search bug.
  • Fixed coordinate bond assigning bug.
  • Removed concept of site copies - all now counted separately.

0.7.0

7 February, 2019
  • Added parsing of large .cif structures.
  • Added visualisation of coordinate bonds.
  • Main chain atoms will now be visible if liganding.
  • Added coordination numbers for multi-metal sites.
  • Groups now have own page.
  • Added browsing by family.
  • Chain sequences now annotated with binding residues and spacers.
  • Images now downloadable.
  • ZincSites can now be searched by family or residue name.

0.6.3

19 December, 2018
  • Added coordination numbers.
  • Improved liganding atom detection.
  • Fixed HTML minification issues.
  • Added browse link on home page.

0.6.2

14 October, 2018
  • Improved bind site cluster algorithm.
  • Binding site residue codes now omit HET ligands.
  • Improved pagination UI.
  • Added option to sort search results.

0.6.1

19 September, 2018
  • Fixed bug in NGL metal selector generation.
  • Fixed bug in metal residue ID generation.
  • Improved functional tests.

0.6.0

14 September, 2018
  • Spurious zinc atoms now excluded (though still logged).
  • Added reasons for when zincs are excluded on PDB page.
  • ZincSites now have residue codes associated for classification.
  • Added BLAST expect value parameter.
  • API now lets you search.
  • Added new data charts.
  • Certain ZincSites now flagged as 'representative' to allow analysis to easily exclude duplicates.

0.5.1

23 August, 2018
  • Fixed links on API page.
  • Fixed title on data browsing page.

0.5.0

7 August, 2018
  • Data generation now uses low energy biological assemblies in place of asymmetric units.
  • Added basic REST API.
  • Added data browsing.
  • Added option to download all data.
  • Added concept of symmetrical copies of a binding site.
  • Database now tracks zinc atoms not suitable for inclusion in a binding site.
  • Fixed bug in numerical searches.

0.4.3

28 June, 2018
  • Added help page with use cases.
  • Added search suggestions in advanced search.

0.4.2

24 June, 2018
  • 3D display now handles atom occupancy.
  • 3D display now shows only relevant atom distances.
  • Added proper 404 page style.
  • Improved 3D display controls layout.
  • Charts/data page now takes 0.4 seconds to load rather that 1.0 seconds.

0.4.1

17 June, 2018
  • You can highlight metals and residues in the 3D display now.
  • Structure spinning.
  • Added attributions.
  • Remove waters from 3D display if not liganding.
  • Minor style fixes.

0.4.0

10 June, 2018
  • Redesigned site look and feel.
  • Improved bind site detection algorithm.
  • Added chains to database and clustered them.
  • Zinc Sites are now clustered based on chain sequence identity.
  • You can now BLAST search the database.
  • Added more advanced search terms, such as resolution.
  • Added PDB keywords.
  • Added distinct PDB pages showing all sites in that PDB.
  • Added controls to 3D display.
  • 3D display now shows contacts.

0.3.0

28 January, 2018
  • Database now only includes zinc sites which interact via side chains.
  • Information on hydrophobic environment now included.
  • Added more search criteria.
  • Added more data visualisation.
  • Improved 3D display to include other zinc sites (and general big fixes).
  • Added links to sites from the same PDB class.

0.2.0

8 January, 2018
  • Added site information on resolution, R-factor, classification, organisms and experimental technique.
  • Added 3D visualisation of the binding sites.
  • Integrated geometry information to site pages.
  • Added links to similar sites to site pages.
  • Built advanced search tool to complement the general search bar.
  • Improved statistics and data visualisation.
  • Improved general look and feel.
  • Redefined database relationships.

0.1.0

13 November, 2017
  • Built initial database of zinc binding sites.
  • Added home page, data page, and basic site structure.
  • Added basic searching of Zinc IDs.