“…The ligand binding sites mapped using one or many crystal structures can be applied to several sequences and be reliable, as long as the protein sequences have similar function and sequence similarity greater than 30%, a typical cut off for protein modelling. Other very useful similar tools exist online, but they have limitations related to showing the binding sites of the sequence (e.g., XSult [20] or Alignment-Annotator web server [36]) or they have limited annotations (e.g., the SwissRegulon database of genome-wide annotations of regulatory sites currently has only 17 prokaryotes and 3 eukaryotes in their collection [37,38]. Thus, the proposed MSALigMap tool is novel and not limited in capabilities in terms of showing the binding sites in the sequence output for protein-ligand, protein-peptide, and protein-DNA complexes.…”