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

Citation
A. Thomas et al., Pex, analytical tools for PDB files. I. GF-Pex: Basic file to describe a protein, PROTEINS, 43(1), 2001, pp. 28-36
Citations number
11
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Biochemistry & Biophysics
Journal title
PROTEINS-STRUCTURE FUNCTION AND GENETICS
ISSN journal
0887-3585 → ACNP
Volume
43
Issue
1
Year of publication
2001
Pages
28 - 36
Database
ISI
SICI code
0887-3585(20010401)43:1<28:PATFPF>2.0.ZU;2-1
Abstract
Pex are created to extract numeric and string descriptions of protein struc tures from PDB files. This concerns covalent bond lengths and angles, secon dary structures, residues in interaction, H-bond lengths and geometry, etc. Several kinds of Pex are generated: (1) general feature (GF-Pex); (2) H-bo nd (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. U sing the GF-Pex of 131 proteins, we analyze the mean residue frequencies, t he phi/psi distribution and the major kinds of secondary structures in prot eins. Thomas et al. (this issue) analyzes the main chain H-bonds in those p roteins. The GF-Pex and H-Pex files of the 131 proteins can be down loaded from the CBMN site (http://www.fsagx.ac.be/bp/). Proteins 2001;43:28-36. (C ) 2001 Wiley Liss, Inc.