structural biology


A system for storing high value protein structure and ligand-complex data internally.

Disseminate to colleagues using familiar tools

Based on world famous PDBsum system.

Promotes internal collaboration with researchers from other groups;

  1. chemoinformaticians

  2. medicinal chemists

  3. biologists

ebisu group

chemogenomix © 2012


The public version of PDBsum is both a collection of software packages and a resulting web site. At the dawn of the internet, PDBsum was one of the first sites to offer meaningful and accessible information about protein 3D structures and their ligand complexes.

Over the years more software components were added to produce a sophisticated web site for interpretting public data that hosts thousands of web queries per month.

It therefore seemed logical to make this same software package available to researchers for storing and displaying proprietary 3D structural data, whether produced by x-ray crystallography, NMR spectroscopy, Homology Modelling or Docking experiments.

The resulting web data is excellent for collaboration with computational and medicinal chemists as it teases out the key points of a protein complex for an intial view and avoids the requirement for specialist 3D viewing software. And when combined with other electronic efforts and can essentially form a 3D structure component of an Electronic Lab Notebook.

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

The public version of PDBsum is hosted at the European Bioinformatics Institute in Prof. Janet Thornton’s group.

Top Page

Simple Overview of Structure with detailed quality interpretation through web implemented Procheck. Summary of publication, Gene Ontology and other data.

Protein Tab

Secondary structure wiring diagram, topology, domain interpretation and structural motifs

Ligand Tab

Ligand interactions through a variety of diagrams produced by Ligplot

Clefts Tab

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

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