Pex, Analytical Tools For Pdb Files. I. Gf-Pex: Basic File To Describe A Protein

Pex are created to extract numeric and string descriptions of protein structures
from PDB files. This concerns covalent bond lengths and angles, secondary
structures, residues in interaction, H-bond lengths and geometry, etc. Several
kinds of Pex are generated: (1) general feature (GF-Pex); (2) H-bond (H-Pex); and
(3) accessible surface (AS-Pex) and force potential (FP-Pex). We describe the
general principles of Pex and detail the GF-Pex files. Using the GF-Pex of 131
proteins, we analyze the mean residue frequencies, the straight phi/psi
distribution and the major kinds of secondary structures in proteins. Thomas et
al. (this issue) analyzes the main chain H-bonds in those proteins. The GF-Pex
and H-Pex files of the 131 proteins can be downloaded from the CBMN site
(http://www.fsagx.ac.be/bp/).