LoopDB - CDR-like loops from the PDB

A collection of loop like PDB structures that satisfy the CDR loop criteria. We use a set of programs to scan the Protein Databank for structures that contain loops that look like these seen in the CDR loops of antibodies. This file is a python pickle file, designed to be used in the neural network found here: https://github.com/OniDaito/MRes To generate this file yourself, you need to perform the following commands, assuming you have installed the required tools. These commands can be performed on Linux or MacOSX (Windows is not supported yet).<br> <pre><code>./buildloopdb -m 5 -x 28 &lt;path to pdb mirror dir&gt; out.db for i in `ls &lt;PATH TO PDBS&gt;`; do ./scanloopdb out.db &lt;PATH TO PDBS&gt;/$i &gt;&gt; summary.txt; done ./extract.sh &lt;path to summary file&gt; &lt;path to PDB Mirror&gt; &lt;path to output files&gt; python pdb_to_postgres.py &lt;dbname&gt; &lt;path to pdbs&gt; python batcher.py --dbname loopdb --out test.pickle --max 28</code></pre> For more details, please look at the Git repository README file you can find here: https://github.com/OniDaito/MRes/blob/master/data/README.markdown