Pex, analytical tools for PDB files. I. GF-Pex: basic file to describe a protein

Abstract

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/). Proteins 2001;43:28-36.