[BioPython] Bio.PDB article in Bioinformatics

[Thomas Hamelryck]

Hi everybody,

An application note describing Bio.PDB (the Biopython PDB parser and related 
code dealing with crystal structures) just appeared in Bioinformatics. For 
reference and abstract see below.

Regards,

-Thomas

----

Bioinformatics. 2003 Nov 22;19(17):2308-10.

PDB file parser and structure class implemented in Python.

Hamelryck T, Manderick B.

Department of Cellular and Molecular Interactions, Vlaams Interuniversitair 
Instituut voor Biotechnologie (VIB) and Computational Modeling Lab (COMO), 
Department of Computer Science, Vrije Universiteit Brussel (VUB), Pleinlaan 
2, 1050 Brussels, Belgium.

SUMMARY: The biopython project provides a set of bioinformatics tools 
implemented in Python. Recently, biopython was extended with a set of modules 
that deal with macromolecular structure. Biopython now contains a parser for 
PDB files that makes the atomic information available in an easy-to-use but 
powerful data structure. The parser and data structure deal with features 
that are often left out or handled inadequately by other packages, e.g. atom 
and residue disorder (if point mutants are present in the crystal), 
anisotropic B factors, multiple models and insertion codes. In addition, the 
parser performs some sanity checking to detect obvious errors. 
AVAILABILITY: The Biopython distribution (including source code and 
documentation) is freely available (under the Biopython license) from 
http://www.biopython.org

---
Thomas Hamelryck
Computational modeling lab (COMO)
Vrije Universiteit Brussel (VUB)
Belgium
http://homepages.vub.ac.be/~thamelry