 |
 |
 |
Simple Atom Depth Index Calculator |  |
 |
|
|
|
Simple Atom Depth Index Calculator | |
|
© 2004-2005 by Daniele Varrazzo
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
Atom depth has been considered as a structural descriptor to correlate protein structure with folding and functional properties. The distance between an atom and the nearest water molecule or the closest surface dot has been proposed as a measure of the atom depth, but, in both cases, the three-dimensional character of depth is largely lost: an atom located at the bottom of a pocket may be at the same distance from the protein surface of an atom located in a protruding loop, but the former will be less accessible than the latter.
SADIC implements a new algorithm to calculate atom depth: it calculates the intersection between the molecular volume and spheres centered on the atoms whose depth has to be quantified. SADIC takes PDB files as input and can emit different measurements of exposed surfaces and volumes as well as a novel depth index, designed to promote comparison between atoms in a molecule and in different molecules.
|
|
|
Simple Atom Depth Index Calculator | |
|