I have always used PDBsum to do a quick look at Ligplot and Nucplot outputs to see which residues in a protein are interacting with a ligand or with DNA. However, I recently found out that sometimes the Nucplot output isn't completely reliable - for the complex structure 6JBX, for example, all interactions are shown as if they were water mediated, which is not the case - there are many direct interactions between residues in the protein and the DNA double helix in the structure.
Are there other options for software that read a PDB file (or webservers that take a PDB code) and report which residues are interacting with DNA (ideally if they specify if the interaction involves the base, the sugar and/or the phosphate)?
Dear Lucas,
You can use "BIOVIA Discovery Studio Visualizer" to visualize the ligand interaction region (https://discover.3ds.com/discovery-studio-visualizer-download). And you can use VMD and PyMOL also.
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