Saladin Adrien, Fiorucci Sébastien, Poulain Pierre, Prévost Chantal, Zacharias Martin
Computational Biology, School of Engineering and Science, Jacobs University Bremen, 28759 Bremen, Germany.
BMC Struct Biol. 2009 May 1;9:27. doi: 10.1186/1472-6807-9-27.
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.
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.
大分子对接是生物信息学中一个具有挑战性的领域。开发新算法是一个缓慢的过程，通常涉及一些常规任务，这些任务应该存在于一个强大的库中，而不是为每个新的软件应用程序都从头编写代码。
我们展示了一个面向对象的Python/C++库，以帮助开发新的对接方法。该库包含诸如PDB格式操纵函数等底层例程，以及用于对接和分析结果的高级工具。我们还通过三体对接程序的详细实现来说明该库的易用性。
PTools库可以处理粗粒度或原子分辨率的分子，并允许用户快速开发新软件。该库已用于通过ATTRACT程序进行蛋白质-蛋白质和蛋白质-DNA对接以及模拟分析。该库根据GNU GPL许可免费提供，并附有详细文档。
