patchdock

[umber]

anyone can plz guide me how to analyze the result of patch dock??????

[blancha]

Read the manual ?

I think you should read this tutorial on how to post questions on a forum first though.

https://www.biostars.org/p/75548/

If you do want help helpful information about analyzing Patch Dock results, you can open PDB files with Pymol.

https://www.pymol.org

http://bioinfo3d.cs.tau.ac.il/PatchDock/help.html

Output
The ouput of PatchDock is a list of candidate complexes between user specified receptor and ligand molecule. The list is presented to the user in the format of a table, each table line represents one candidate complex.

Table Format:

Solution No: Number of the solution
Score: Geometric shape complementarity score (see reference 1 for details). The solutions are sorted according to this score.
Area: Approximate interface area of the complex.
ACE: Atomic contact energy according to Zhang et al. (see reference 2).
Transformation: 3D transformation: 3 rotational angles and 3 translational parameters. The transformation should be applied on the ligand molecule.
PDB file of the complex: The predicted complex structure in PDB format.

Download PDB files with complexes:

In addition, the server provides an option to download up to 100 top ranking candidate complexes in the PDB format in one zipped file. The user may specify the number of solutions and the server will prepare a Zip file for download.