Improved performance and interface with Jmol Affinity Inspector now loads all the protein-DNA and protein-RNA crystal structures from the PDB significantly faster. The improvements in the performance and interface allow users to quickly search through different structures that contain similar proteins from the same protein family or superfamily in order to find the biochemical mechanisms that distinguish differences in specificity. The Needleman-Wunsch global alignment between the amino acid sequences from the crystal structure and affinity model allows users to quickly ascertain how well the crystal structure matches the binding properties of the protein from the binding experiment within different regions of the structure.