Before revision:  Each binding site is represented in a d-dimensional vector form. The 3D structures of binding sites are mapped to vector form such that similar binding sites hash into proximal localities, and dissimilar sitesfall across diverse regions. A sensitivity analysis of rotation and perturbation and validation study is performed to understand the behavior of the method . Benchmarking exercises have been carried out against state of the art binding site comparison methods on state of the art datasets.
After revision:  The method is based on pairwise distances between representative points and chemical compositions in terms of constituent amino acids of a site. The vector embedding serves as a locality sensitive hash function for proximity queries and determining similar sites. The method has been the top performer with more than 95\% quality scores in extensive benchmarking studies carried over 10 datasets and against 23 other site comparison methods on state of the art datasets.