I don't know which one is the 'best', but the following databases are in my lists:

• hPDI: a database of experimental human protein-DNA interactions. http://www.ncbi.nlm.nih.gov/pubmed/19900953 download: http://bioinfo.wilmer.jhu.edu/PDI/download/download.html
• BIPA: a database for protein-nucleic acid interaction in 3D structures http://www.ncbi.nlm.nih.gov/pubmed/19357098 download: http://mordred.bioc.cam.ac.uk/~semin/BIPA/
• UniPROBE: an online database of protein binding microarray data on protein-DNA interactions. http://www.ncbi.nlm.nih.gov/pubmed/18842628 download http://thebrain.bwh.harvard.edu/uniprobe/downloads.php
• (...)

Hi Kei,

I don't know what is best and most appropriate for your need but here are a few more:

• DBD
• PRODORIC
• cTFbase (for cyanobacteria)

Cheers,
Magali

Most (but not all) protein-DNA involve transcription factor based activation. TRANSFAC is probably the most well known database of protein to gene targets.

I'm assuming if you want to visualize networks that you are looking for DBs that have data on protein-DNA interactions in the form of specific Transcription Factor -> Target Gene relations, rather than information about the overall DNA binding specificity of TFs (e.g. UniProbe, hDPI, Jaspar).

If so then ORegAnno and Pazar are probably your best bet for curated Transcription Factor -> Target Gene data. Both have APIs (ORegAnno and Pazar) and XML dumps. I think Pazar is a more active currently, and has the virtue of being a portal for many other datasets (including ORegAnno), so this may the better choice for your purposes.