PTools: an opensource molecular docking library

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.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.Most biological processes in the cell involve macromolecules interacting with one or several partners [1]. Knowledge of the overall structures of these assemblies as well as the details of the interactions is essential for understanding the underlying biological mechanisms or for developing new therapeutic strategies. In spite of spectacular progress, the determination of the three-dimensional structure of large complexes at atomic resolution by means of X-ray crystallography or nuclear magnetic resonance spectroscopy remains a difficult task. Even in the case of binary complexes (two macromolecular partners), the number of available structures only represents a minor fraction of the complexes known to exist. Given the deficit of structural information on these assemblies and the increasing number of available structures for isolated proteins, computational modeling tools provide a promising approach to predicting structures of protein complexes. Docking methods are increasingly reliable and efficient for assembling macromolecular complexes when the partners do not present any large internal deformation. Numerous studies have been dedicated to protein-protein interactions [1] and the worldwide challenge "Critical Assessment of PRedicted Interactions" (CAPRI) [2-4] demonst