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PTools: an opensource molecular docking library

Adrien Saladin12, Sébastien Fiorucci14, Pierre Poulain3, Chantal Prévost2* and Martin Zacharias1*

Author Affiliations

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

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BMC Structural Biology 2009, 9:27  doi:10.1186/1472-6807-9-27

Published: 1 May 2009

Abstract

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.