Summary of Antibody Structures in the Protein Databank

Last updated 22.12.15

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Introduction

This page provides an automatically updated summary of all antibody structures in the Protein Databank

Given the problems with parsing out useful information from PDB files in an automated fashion, there may be some errors in these summaries. We would be grateful if users would notify us ( ) if any such problems are found!

Methods

We mirror PDB files here at Reading and use a Make based system for automatic processing of new PDB files as they arrive. You can download a simplified Makefile which demonstrates how to process every file in the PDB.

As part of this processing, a Perl script is used to determine whether a file is an antibody. If so, summary information about that antibody is extracted from the file using Perl and C programs and the results are written in XML. At this stage, manual correction of errors detected in the automatic processing can be performed.

Individual XML files are concatenated into a master file containing information on all the antibodies. XSLT is then used to create a summary view of all antibodies or a detailed view of a single antibody on the fly as you view the pages.

If you use this site, please site: Allcorn, L. C. and Martin, A. C. R. (2002) SACS - A Self-Maintaining Database of Antibody Crystal Structures, Bioinformatics, 18, 175-181. [PDF]

Credits

The design of these pages, and the Perl programming was done by Lee Allcorn ( ), an undergraduate project student at Reading University.

The project specification, C programming (to extract experimental data and loop information) and XSLT programming was done by Andrew Martin ( ).


Get the XML file