{"id":1231,"date":"2013-10-06T23:11:54","date_gmt":"2013-10-06T22:11:54","guid":{"rendered":"http:\/\/www.blopig.com\/blog\/?p=1231"},"modified":"2014-02-06T07:37:09","modified_gmt":"2014-02-06T07:37:09","slug":"get-pdb-intermolecular-protein-contacts-and-interface-residues","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2013\/10\/get-pdb-intermolecular-protein-contacts-and-interface-residues\/","title":{"rendered":"Get PDB intermolecular protein contacts and interface residues"},"content":{"rendered":"

<\/code> Very often in Struc Bio it is necessary to determine the contacts between two molecules. Most of us in the group have written a snippet of code to compute precisely that or they have adapted the Biopython<\/a> functionality or one of the tools in pdbtools<\/a>. The piece of code written in Python presented here is a Biopython variety that gives you the intermolecular contacts and it annotates the interface neighborhood. An example of the program output is given in the Figure below:<\/p>\n

\"The<\/a>

The complex between an antibody and an antigen is shown on the left without the annotation. On the right it is shown with intermolecular contacts annotated in red (4.5A distance) and the interface neighborhood shown in green (10A away from any contact residue).<\/p><\/div>\n

Download<\/strong><\/p>\n

You can download it from here<\/a>. There are three files inside:<\/p>\n

    \n
  1. GetInterfaces.py – the main source\/runnable file<\/span><\/li>\n
  2. README.txt – instructions, very similar to this post (quite a lot copy\/pasted)<\/li>\n
  3. 1A2Y.pdb – the PDB file used in the example to practice on.<\/li>\n<\/ol>\n

    Requirements:<\/strong><\/p>\n

    You need Biopython<\/a>. (if you are from OPIG or any other Bioinformatics group, most likely it is already installed on your machine). You can download it from\u00a0here<\/a>.<\/p>\n

    How to use it?<\/strong><\/p>\n

    As the bare minimum, you need to provide the structure of the pdb(s) and the chains that you want to examine contacts in.<\/p>\n

    Input options:<\/p>\n