PTools: An opensource molecular docking library

Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost, Martin Zacharias

Research output: Contribution to journalArticlepeer-review

32 Scopus citations

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.

Original languageEnglish
Article number27
JournalBMC Structural Biology
Volume9
DOIs
StatePublished - 2009
Externally publishedYes

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