2015 Volume 8 Pages 9-13
We developed a new application to quantitatively evaluate the sequence conservation of ligand-binding sites by integrating information pertaining to protein structures, ligand-binding sites, and amino acid sequences. These data are visualized onto protein structures via a Jmol or PyMOL interface. The visualization is very important for structure-based drug design (SBDD). Key features of this application are the visualization of slight differences in specific ligand-binding sites and ConservationScore comparable among ligand-binding sites. Furthermore, we conducted an experiment to visualize the calculation and comparison of the ConservationScore of four viral proteins as well as an experiment to visualize the differences between proteins belonging to the human β adrenergic receptor family. This application is available at http://www.bio.gsic.titech.ac.jp/visco.html.