CX

 Protrusion index
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Help and guidelines on CX
 
Contents
 
  1. Overview
  2. Method
  3. Input file
  4. Output file
  5. Options
Overview
CX is a simple and fast algorithm that calculates a protrusion (or convexity) index (cx) for atoms in protein structures. As output files can be directly displayed by standard molecular graphics programs, CX can be used for the visual inspection of proteins, protein/ligand and protein/protein complexes in a straightforward manner.

Protruding regions are good candidates as proteolytic cleavage sites and antigenic determinants.

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Method
For each heavy (non-hydrogen) atom in a protein structure, the program counts the number of atoms within a fixed distance R (the default value is 10 A). The number of atoms within the sphere is multiplied by the mean atomic volume found in proteins (20.1 +/- 0.9 A^3), which gives the volume occupied by the protein within the sphere, Vint. The remaining volume of the sphere, Vext, is calculated as the difference between the volume of the sphere and Vint. The cx value is then defined as Vext/Vint. Atoms in protruding regions will have a high ratio between the external and the internal volume, i.e. a high cx. Slightly negative values that can be observed occasionally for buried atoms, are reset to zero. For protein structures, you can expect cx to vary between 0 and 15. Be aware that CX is not designed to identify cavities, clefts, or concavity regions.
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Input file
CX reads standard PDB coordinate files as the input. The program reads only ATOM lines. Thus, HETATM lines describing non standard residues, cofactors, metal ions, and water molecules are not taken into account. By default, the program treats each chain in the PDB file as an independent molecule (i.e. the atoms of chain B are not taken account when calculating the protrusion index for the atoms of chain A) but the results are written into a single file.
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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 cx value. The output file can be thus displayed using most molecular graphics programs, and atoms colored by their cx value.
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Options
  Sphere radius: the default value is 10.0 L, and works for most of the applications. In some instances, for example if you want to analyze a complex between a large protein and a peptide ligand, it is advisable to use a smaller R value to highlight the peptide features.
  Atomic volume: the default value is 20.1 A^3. Different atom types have different volumes: this value is to be taken as an average.

  Mean residue cx: the default option is "no". If you set it to "yes", the mean residue cx 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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