Bioinformatics Tools Training Program

PatchDock algorithm is inspired by object recognition and image segmentation techniques used in
Computer Vision. Docking can be compared to assembling a jigsaw puzzle. When solving the
puzzle we try to match two pieces by picking one piece and searching for the complementary one.
We concentrate on the patterns that are unique for the puzzle element and look for the matching
patterns in the rest of the pieces. PatchDock employs a similar technique. Given two molecules,
their surfaces are divided into patches according to the surface shape. These patches correspond to
patterns that visually distinguish between puzzle pieces. Once the patches are identified, they can be
superimposed using shape matching algorithms.

The algorithm has three major stages:
Molecular Shape Representation – in this step we compute the molecular surface of the molecule.
Next, we apply a segmentation algorithm for detection of geometric patches (concave, convex and
flat surface pieces). The patches are filtered, so that only patches with ‘hot spot’ residues are
retained.
Surface Patch Matching – we apply a hybrid of the Geometric Hashing and Pose-Clustering matching techniques to match the patches detected in the previous step. Concave patches are
matched with convex and flat patches with any type of patches.

Filtering and Scoring – the candidate complexes from the previous step are examined. We discard
all complexes with unacceptable penetrations of the atoms of the receptor to the atoms of the ligand.
Finally, the remaining candidates are ranked according to a geometric shape complementarity score.

Flowchart
1. Open patchdock
2. Input Receptor File
3. Input Ligand File
4. RMSD (Default 4.0)
5. Input Email id
6. Choose Complex (Protein-Small Molecule, Antigen-Antibody,enzyme-inhibitor,Default)
7. Submit.
You will get the result or solution file on the given email id in respective time