PocketAlign

About PocketAlign: Comparison of binding sites helps identify functional similarities and also identify drug cross-reactivities.
PocketAlign encodes shape descriptors in the form of geometric perspectives, supplemented by chemical group classification of the binding site residues. The shape descriptor considers several perspectives with each residue as the focus and captures relative distribution of residues around it in a given site.
Residue-wise pairings are computed by comparing the set of perspectives of the first site with that of the second and using a greedy approach that incrementally combines residue pairings into a mapping.
The mappings in different frames are then evaluated by different metrics encoding extent of alignment of individual distance elements. Different initial seed alignments are computed, each subsequently extended by detecting consequential atomic alignments in a three dimensional grid, and the best 500 stored in a database.

Upload two PDB files: Please input complete residues (all amino-acid heavy atoms) for each pocket. Please follow the PDB file format. Example pockets are given below:

Alignments are then ranked based on Qscores and the top scoring alignments reported. The alignments are then streamed into Pymol to enable their visualization and analyses. Please note that due to the heuristic nature of the algorithm, an A-to-B alignment will yield different results from a B-to-A alignment, where A and B are any two pockets. The algorithm is implemented as stand-alone and web-based software packages and made available to the community:

References:

Reference #1: Yeturu, Kalidas, and Nagasuma Chandra. "PocketAlign a novel algorithm for aligning binding sites in protein structures." Journal of chemical information and modeling 51.7 (2011): 1725-1736.