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The protein surface for 1ett and active site hydrophobic regions calculated by SiteMap are shown here. In tests across 274 protein structures taken from the PDB, SiteMap correctly identifies 94% of all ligand binding sites. Furthermore, for submicromolar binding sites, SiteMap's accuracy improves to 98%.

SiteMap: Fast, accurate, and practical binding site identification

Combining a novel algorithm for rapid binding site identification and evaluation with easy-to-use property visualization tools, SiteMap provides researchers with an efficient means to find and better exploit the characteristics of ligand binding sites.

The importance of understanding protein sites

Understanding the structure and exploiting the function of protein active sites is a cornerstone of drug design. Doing so requires chemists to know the location of these sites, yet at the outset of many drug design projects the location of a binding site for protein-ligand or protein-protein interactions remains unknown. Additionally, it is equally important to identify the locations of any potential allosteric binding sites.

SiteMap's proven algorithm for binding site identification and evaluation can help researchers to locate binding sites with a high degree of confidence and predict the druggability of those sites. Beyond lead discovery, SiteMap assists in lead optimization by providing insight into ligand-receptor interactions so as to suggest effective strategies to modify lead compounds to enhance receptor complementarity.

 

Works to Cite

Halgren, T., "Identifying and Characterizing Binding Sites and Assessing Druggability," J. Chem. Inf. Model., 2009, 49, 377–389.

Halgren, T., "New Method for Fast and Accurate Binding-site Identification and Analysis," Chem. Biol. Drug Des., 2007, 69, 146–148.