PTools: an opensource molecular docking library.
BACKGROUND
Macromolecular docking is a challenging field of bioinformatics. Developing new algorithms is a slow process generally involving routine tasks that should be found in a robust library and not programmed from scratch for every new software application.


RESULTS
We present an object-oriented Python/C++ library to help the development of new docking methods. This library contains low-level routines like PDB-format manipulation functions as well as high-level tools for docking and analyzing results. We also illustrate the ease of use of this library with the detailed implementation of a 3-body docking procedure.


CONCLUSIONS
The PTools library can handle molecules at coarse-grained or atomic resolution and allows users to rapidly develop new software. The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis. This library is freely available under the GNU GPL license, together with detailed documentation.
Saladin
Adrien
A
Computational Biology, School of Engineering and Science, Jacobs University Bremen, 28759 Bremen, Germany. adrien.saladin@ibpc.fr
Fiorucci
Sébastien
S
Poulain
Pierre
P
Prévost
Chantal
C
Zacharias
Martin
M
D022126:Access to Information; D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein / Q000145:classification*; D016247:Information Storage and Retrieval; D007990:Libraries; D011485:Protein Binding; D025941:Protein Interaction Mapping; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein; D012984:Software
D011506:Proteins