PDBsum Proprietary

3D Protein Structure and Ligand complex repository, analysis and communication system


Overview

PDBsumProprietary is excellent for collaboration with computational and medicinal chemists.

  • nstall and run behind your own firewall
  • Facilitate analysis of proprietary 3D structures and ligand complexes.

PDBsumProprietary teases out key points of a protein complex for intial analysis and avoids the requirement for specialist 3D viewing software and knowledge.

Repository

Add all 3D structures determined in-house, by either x-ray or NMR experiments or predictive homology models. Preview the full functionality of PDBsumProprietary by simply looking at the public version of PDBsum which processes all public PDB structures at the European Bioinformatics Institute (see links in examples below).



Clicking following these images will take you through to the real example pages at the EBI.



Top Page

Simple Overview of Structure including detailed quality interpretation through web implemented Procheck and Ramachandran plot.

 

Protein Tab

Secondary structure wiring diagram, topology, domain interpretation and structural motifs all within a single browser tab

 

Ligand Tab

Ligand interactions through 2D summary diagrams produced by Roman Laskowski's Ligplot

 

Clefts Tab

Cleft Volumes as calculated by Surfnet. Accessible and buried vertices, cleft depth and associated data highlighted


Data Input

Data can be input in two ways. 

Completed structures are introduced through a pipeline script that is excecuted as a cron job at regular intervals that suits your work requirements. Alternatively, if you want to take a quick look at an interim structure file, perhaps during the refinement process or to check whether a homology model makes sense, you can use the Generate function will allow just you to see a temporary set of web pages. These temporary pages are then cleared according to a schedule chosen by your group.

 

3D Viewing

Although the focus of this web site is simple 2D viewing, various features can also the 3D enabled using JMol or RasMol for quick analysis.

 

Public Version of PDBsum

A quick reminder that the public version of PDBsum is hosted at the European Bioinformatics Institute in Prof. Janet Thornton’s group.