While reading DNAproDB: an expanded database and web-based tool for structural analysis of DNA–protein complexes, I noticed SNAP and DSSR being mentioned. The detailed citations are as below:

Information about individual nucleotide–residue interactions is also provided, such as hydrogen bonding, interaction geometry (based on SNAP (10)), buried solvent accessible surface areas and identification of the interacting residue and nucleotide moieties …

DNAproDB assigns a geometry for every nucleotide–residue interaction identified using SNAP, a component of the 3DNA program suite (10). The residues for which probabilities are shown are those with planar side chains so that a stacking conformation can be defined.

Base pairing and base stacking between nucleotides are identified using the program DSSR (20).

SNAP and DSSR are two (relatively) new programs in the 3DNA software suite. As the author, I am always glad to see them being cited explicitly in literature. The fact that SNAP and DSSR are cited together by DNAproDB, however, is especially significant. I am aware of the initial version of DNAproDB, but I definitely like the updated one better. This is what I recently wrote in response to a question on the 3DNA Forum:

Regarding DNA-protein interactions in general, you may want to have a look of DNAproDB from the Remo Rohs laboratory. A new paper has just been published in NAR, ‘DNAproDB: an expanded database and web-based tool for structural analysis of DNA–protein complexes’.

I’ve no doubt that SNAP and DSSR would be widely used in applications related to DNA/RNA structural bioinformatics. DSSR (to a lesser extent, SNAP) represents my view of what a scientific software tool should be.





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