Comparison of Structure-based Tools for the Prediction of Ligand Binding Site Residues in Apo-structures

In this paper, a group of structure-based algorithms used in the prediction of ligand binding sites in proteins were tested on apo-structures, and their results are analyzed and discussed. In particular, we focused on the accuracy of predicting the residues at the binding sites as the main criterion for comparison. The data set used for the testing was compiled using the LigASite database and consisted entirely of apo-structures. The tools compared are LIGSITE, SURFNET, DEPTH, GHECOM, SiteHound, and Fpocket.