Before revision:  Benchmarking exercises have been carried out against state of the art binding site comparison methods on state of the art datasets. The exercises validate our proposed method and demonstrate that the proposed method is rotationally invariant and can handle natural perturbations expected in the biological system.
After revision:  Benchmarking exercises have been carried out against state of the art binding site comparison methods . The algorithm serves for high throughput processing and has been evaluated for stability with respect to reference frame shifts, coordinate perturbations and residue mutations. We provide Site2Vec as a stand alone executable and a web service hosted at URL