This article is part of the supplement: The 2008 International Conference on Bioinformatics & Computational Biology (BIOCOMP'08)
PDA: an automatic and comprehensive analysis program for protein-DNA complex structures
Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223 USA
BMC Genomics 2009, 10(Suppl 1):S13 doi:10.1186/1471-2164-10-S1-S13Published: 7 July 2009
Knowledge of protein-DNA interactions at the structural-level can provide insights into the mechanisms of protein-DNA recognition and gene regulation. Although over 1400 protein-DNA complex structures have been deposited into Protein Data Bank (PDB), the structural details of protein-DNA interactions are generally not available. In addition, current approaches to comparison of protein-DNA complexes are mainly based on protein sequence similarity while the DNA sequences are not taken into account. With the number of experimentally-determined protein-DNA complex structures increasing, there is a need for an automatic program to analyze the protein-DNA complex structures and to provide comprehensive structural information for the benefit of the whole research community.
We developed an automatic and comprehensive protein-DNA complex structure analysis program, PDA (for
PDA is a computational tool for structural annotations of protein-DNA complexes. It provides a useful resource for investigating protein-DNA interactions. Data from the PDA analysis can also facilitate the classification of protein-DNA complexes and provide insights into rational design of benchmarks. The PDA program is freely available at http://bioinfozen.uncc.edu/webpda webcite.