Pacgum: Estimator of Protein Packing Quality

This is a new (as of 2007) technique for checking the packing regularity of a 3D protein model. The score it returns strongly correlates with the resolution and the R factor of crystal structures, but can be computed for any protein structure, including NMR structures and homology-based models.

We recommend using this as a validation tool, in complement to other tools, when the resolution of a protein structure is unknown (NMR, theoretical models) or suspicious. Current modelling programs do not optimize this score yet, and when they do, we hope it will genuinely improve the quality of the protein models.

Submission form

Enter PDB ID: or upload your own PDB file:

Optional query name:

Output format:
HTML
JSON, with optional JavaScript callback:

Privacy notice: uploaded protein models are not stored on our server, but only the results of their automatic analysis, which does not allow model reconstruction by a third-party. However data transfer is not encrypted and submitting confidential data is done at your own risk.

JSON API

For single-protein studies, this interface can be used easily by remote programs using the JSON interface that we provide. Here is the list of the available CGI parameters and their meaning:

• pdbid: a 4-letter PDB code. PDB files are downloaded from the PDB site, so it always takes a while.
• pdbfile: the uploaded protein model in the PDB format. The pdbid and pdbfile parameters are mutually exclusive. Only the first model of multi-model structures (e.g. NMR) will be considered.
• name: a name for the query. It is optional and defaults to the automatically-assigned ID.
• output: the output format. This is optional but defaults to html. For JSON output, set it to json.
• callback: the name of a JavaScript function to call with the JSON result as argument, for use with dynamic <script> elements.

These are the 3 kinds of results that can be obtained:

• Success: http://biomics.burnham.org/pacgum?pdbid=1crn&output=json
• Failure: http://biomics.burnham.org/pacgum?pdbid=9crn&output=json
• Malformed query: http://biomics.burnham.org/pacgum?pdbid=11crn&output=json

About

This tool derives from findings by Martin Jambon in Adam Godzik's lab, with the help of Boguslaw Stec and Marilisa Leone. More details can be found in the results pages.

For faster, large-scale analyses you may want to obtain a local copy of the software. In that case, please contact us.

Pacgum is the pseudo-English name for pac-gommes, the French name for power-pellets in the Pac-Man animation series inspired by the Japanese video game.