Implementation Details of Evaluated Methods.

This table summarizes the details of each step of the ligand binding site prediction process for the methods we evaluate. The new ConCavity methods are based entirely on our code. We also developed new implementations (Ligsite+, PocketFinder+, and Surfnet+) of three previous methods. Predictions for the other previous methods were obtained from the listed publicly accessible web servers. These servers output sets of residues associated with predicted binding pockets. For inclusion in the residue prediction evaluation, the output of these servers was post-processed as specified. This step is not necessary for our methods, because Blur outputs ranked residue predictions. A “+” appended to the method name indicates that it is based (at least in part) on our code. Implementation details of each algorithm are given in the text, and code for our implementations is available online.