Specialized computer software was developed to extract the effective atomic intefaces of protein-DNA complexes and to classify their interaction types (for details about the definition of effective atomic interactions see ). The analysis of effective atomic interactions is useful to better characterize and describe the common and unique features present at different complex interfaces, which in turn could help to dilucidate the key specificity determinants involved in a particular protein-DNA recognition process.
The software is composed of main and supporting applications written in C++ for command-line execution. These applications are highly customizable, take PDB files as input and different options. There are two main applications: one is used to analyse any kind of atom-atom contact, where the user can define atom types, centroids (i.e. average of several atom positions) and distance ranges; in the other application, the user can also define the type of interaction that any pair of atoms may have (e.g. hydrogen bonds, hydrophobic interactions, etc.). These analyses may be done including water molecules, and also a new approach to detect the effective atomic interactions at the complex interface . According to the options selected, the output of the software may be the contact matrices, and files with detailed information about interactions.
You can download the software here:
-Command-line interface (CLI), such as UNIX Shell, MacOS X Terminal, MS-DOS Prompt.
1. Ferrada, E. and Melo, F. (2009) Effective knowledge-based potentials. Protein Science 18, 1469-1485.