PDA: an automatic and comprehensive analysis program for protein-DNA complex structuresReport as inadecuate

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BMC Genomics

, 10:S13

First Online: 07 July 2009


BackgroundKnowledge 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.

ResultsWe developed an automatic and comprehensive protein-DNA complex structure analysis program, PDA for p rotein-D NA complex structure a nalyzer. PDA takes PDB files as inputs and performs structural analysis that includes 1 whole protein-DNA complex structure restoration, especially the reconstruction of double-stranded DNA structures; 2 an efficient new approach for DNA base-pair detection; 3 systematic annotation of protein-DNA interactions; and 4 extraction of DNA subsequences involved in protein-DNA interactions and identification of protein-DNA binding units. Protein-DNA complex structures in current PDB were processed and analyzed with our PDA program and the analysis results were stored in a database. A dataset useful for studying protein-DNA interactions involved in gene regulation was generated using both protein and DNA sequences as well as the contact information of the complexes. WebPDA was developed to provide a web interface for using PDA and for data retrieval.

ConclusionPDA 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.

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Author: RyangGuk Kim - Jun-tao Guo

Source: https://link.springer.com/article/10.1186/1471-2164-10-S1-S13

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