Index of /pubs/zinc

      Name                    Last modified       Size  Description


[DIR] Parent Directory        14-Jul-2007 01:22      -  
[   ] FeatureForMetals.tar.gz 02-Aug-2007 10:27   5.4M  
[TXT] apo-test-set.txt        16-Jul-2007 09:02     1k  
[TXT] calcium_test.pts        16-Jul-2007 09:12     2k  
[TXT] calcium_training.pts    16-Jul-2007 09:11     5k  
[TXT] example-modeller-scr..> 16-Jul-2007 09:17     1k  
[TXT] modeller-templates.txt  16-Jul-2007 09:15     1k  
[TXT] process.py              16-Jul-2007 09:12     1k  
[TXT] test.pts                16-Jul-2007 09:09     3k  
[TXT] training.pts            16-Jul-2007 09:12     9k  
[IMG] zinc_vs_calcium.png     16-Jul-2007 15:25   113k  

Files:

1) FeatureForMetals.tar.gz

Source code distribution (contains installation and usage instructions).

2) training.pts, test.pts

Contain holo proteins used to train and test the zinc model. The files
are tab delimited, and the fields are as follows: biounit PDB
identifier, x coordinate, y coordinate, and the z coordinate, residue.

3) apo-test-set.txt

Contains holo and apo pairs for the apo proteins used to test the zinc
model.

4) calcium_training.pts, calcium_test.pts

These files contain the calcium points used as negative training
examples (calcium_training.pts) and the calcium holo test set
(calcium_test.pts) for the Zn vs. Ca model.

5) modeller-templates.txt

Contains 29 holo proteins and the templates used to model their
structures using MODELLER. The file is tab delimited. The first field
is the holo biounit PDB identifier, the second is the chain, and the
last two fields are the template protein's PDB identifier and chain.

6) example-modeller-script.py

This is an example of a script used to run MODELLER.

7) zinc_vs_calcium.png

The fingerprint of the zinc vs. calcium model.