Software
PTools: an opensource molecular docking library
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* Corresponding authors: Chantal Prévost chantal.prevost@ibpc.fr - Martin Zacharias m.zacharias@jacobs-university.de
1 Computational Biology, School of Engineering and Science, Jacobs University Bremen, 28759 Bremen, Germany
2 LBT, CNRS UPR 9080 and Université Paris Diderot – Paris 7, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
3 DSIMB, Inserm UMR-S665, Université Paris Diderot – Paris 7, Institut National de la Transfusion Sanguine (INTS), 6 rue Alexandre Cabanel, 75015 Paris, France
4 LCMBA, UMR-CNRS 6001, Faculté des Sciences, Université de Nice-Sophia Antipolis, 06108 Nice Cedex 2, France
BMC Structural Biology 2009, 9:27 doi:10.1186/1472-6807-9-27
Published: 1 May 2009Abstract
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.
Conclusion
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.