The additional strength is obtained by the flexible combination of both speed and complexity in the intuitive and thus natural queries to the structural data. The speed is due to the usage of a binary space partitioning (BSP) tree which allows very fast queries in 3D. atoms are treated as vectors), b) the implementation of a query parser that translates queries written in human readable language into a combination of algebra set operations and c) the fact that no additional Python packages are necessary. The simplicity of p3d is due to a) the usage of object oriented programming (i.e. Although similar modules exist as part of the BioPython project or part of the biskit package, p3d was developed in order to offer a Python module that is powerful and fast, yet intuitive to use. p3d is such a module for the Python scripting language. However, such approaches require a rapid development of new structural bioinformatic tools that are adapted to the questions asked, which in turn requires a robust framework or module. ligand binding or can be used to estimate favourable structural configurations that are important for de novo protein design or prediction of protein folding. Such knowledge based approaches can help to identify key parameters in e.g. The increasing number of high-resolution protein structures available in the protein database allows knowledge based approaches by comparing structural features throughout non-redundant protein data sets. P3d is the perfect tool to quickly develop tools for structural bioinformatics using the Python scripting language. All these factors combined facilitate the rapid development of bioinformatic tools that can perform quick and complex analyses of protein structures. p3d's strength arises from the combination of a) very fast spatial access to the structural data due to the implementation of a binary space partitioning (BSP) tree, b) set theory and c) functions that allow to combine a and b and that use human readable language in the search queries rather than complex computer language. P3d is an object oriented Python module that adds a simple yet powerful interface to the Python interpreter to process and analyse three dimensional protein structure files (PDB files). For this the Python scripting language is the optimal choice since its philosophy is to write an understandable source code. The development of such tools requires a robust interface to access the structural data in an easy way. High-throughput bioinformatic analysis tools are needed to mine the large amount of structural data via knowledge based approaches.

What is p3d