DPX

 Depth index
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Help and guidelines on DPX
 
Contents
 
  1. Overview
  2. Method
  3. Input file
  4. Output file
  5. Options
  6. References
Overview
DPX is a simple and fast algorithm that calculates the depth of each atom in a protein structure. As output files can be directly displayed by standard molecular graphics programs, DPX can be used for the visual inspection of the protein interior in a straighforward manner. Atom/residue depth is correlated to the thermodynamic stability of a protein, to the formation of protein/protein complexes, to the H/D amide exchange rates as measured by NMR, to the degree of residue conservation in structurally related protein families, and to amino acid types.
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Method
Atom depth (dpx) is defined as the distance (Angstrom) of a non-hydrogen atom from its closest solvent accessible neighbor, where the atom solvent accessibility is calculated using the rolling sphere algorithm. Therefore, solvent accessible atoms have dpx=0 by definition, buried atoms will have increasing dpx values as one moves towards the core of the protein. Typical dpx values are in the range 0-8 A. The maximum dpx value (dpx(max)) found for a single chain monomeric protein depends in the first instance by the number of residues in the chain. Be aware, however, that different proteins, although having the same number of residues, can display quite different values for dpx(max).
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Input file
DPX reads standard PDB coordinate files as the input. In the present form, DPX is aimed at the analysis of the interior of single chain monomeric protein. Before submission, inspect the PDB file and, if the case, edit it in order to have one single molecule (chain). The program reads only ATOM lines. Thus, HETATM lines describing non standard residues, cofactors, metal ions, and water molecules are not taken into account.
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Output file
The output is a coordinate file in PDB format in which the atomic displacement parameter (B-factor, or temperature factor) is replaced by the dpx value. The output file can be thus displayed using most molecular graphics programs, and atoms colored by their dpx value.
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Options
  Sphere radius: this is the radius of the rolling sphere used to identify accessible and buried atoms. The default value is 1.4 A
  Mean residue dpx: the default option is "no". If you set it to "yes", the mean residue depth value will be computed, and an additional file written. This file contains residue number, residue name, minimum, maximum, average and standard deviation values for each residue.
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References
    The method is explained in:
DPX, for the analysis of the protein core. Pintar A., Carugo O. and Pongor S. Bioinformatics 2003, 19:313-314.

Applications of DPX are described here:
-Atom depth as a descriptor of the protein interior. Pintar A., Carugo O. and Pongor S. Biophys. J. 2003, in press.

Other methods to calculate "depth" and its applications have been described in:
-Residue depth: a novel parameter for the analysis of protein structure and stability. Chakravarty, S. and Varadarajan R. Structure Fold. Des. 1999 7(7):723-32.

-A nuclear magnetic resonance study of the hydrogen-exchange behaviour of lysozyme in crystals and solution. Pedersen T.G., Sigurskjold B.W., Andersen K.V., Kjaer M., Poulsen F.M., Dobson C.M. and Redfield C. J. Mol. Biol. 1991 218(2):413-26.

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