Prot-DNA-Korr is a tool for studying sequence correlations between DNA-binding proteins and their binding sites.
The program searches for such pairs of positions in alignments of proteins and their binding sites that demonstrate correlations between amino acid residues and bases. Such pairs (we call them correlated pairs) may play a biological role in specific 'protein'-'nucleic acid' binding. In particular they may form a specific contacts, which allows the protein to recognize binding sites.
No PDB structures of complexes are required. One only needs two alignments with the same number of elements: one of proteins and one of their respective binding sites. This guide. describes the input format and the procedure of submitting a query.