FiberDock
Flexible Induced-fit Backbone Refinement in Molecular Docking
[Web Server] [About] [Download] [FAQ] [Help] [References]   Contact: ppdock@tau.ac.il
FiberDock is an efficient method for flexible refinement and re-scoring of rigid-body protein-protein docking solutions.

Option 1 (use transformation file)
(Example: Receptor Molecule: 1ukr:A, Ligand Molecule: 1t6g:B, Transformations File:1t6g_trans.txt)
Receptor Molecule: (PDB:chainId e.g. 1ukr:A) or upload file:
Refine receptor's backbone conformation?&nbsp&nbsp&nbsp Yes &nbsp&nbsp&nbsp No
Ligand Molecule: (PDB:chainId e.g. 1t6g:B) or upload file:
Refine ligand's backbone conformation?&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp Yes &nbsp&nbsp&nbsp No
Rigid Docking Solutions: File format: PatchDock transformations file
ZDOCK output file
upload file:
(up to 100 solutions)
* If no file is uploaded a zero-transformation will be used.
Option 2 (use models file)
(Example: Models File:models_example.ent, Receptor chain: E, Ligand chain: I)
Models file: &nbsp Receptor chain: &nbsp Ligand chain: (up to 100 models)
the backbone conformation of the proteins must be the same in all the models!
Refine receptor's backbone conformation?&nbsp&nbsp&nbsp Yes &nbsp&nbsp&nbsp No
Refine ligand's backbone conformation?&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp Yes &nbsp&nbsp&nbsp No

Your e-mail address: (optional)
A link to the results page will be sent to this address when FiberDock will finish running.

If you use this program, please cite:
1. E. Mashiach, R. Nussinov and H. J. Wolfson. FiberDock: Flexible induced-fit backbone refinement in molecular docking. Proteins 2009 Dec 9;78(6):1503-1519.
2. E. Mashiach, R. Nussinov and H. J. Wolfson. FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking. Nucleic Acids Res. 2010 Jul 1;38 Suppl:W457-61.


Advanced Options:   (optional)
[show][hide]

Side-Chain Optimization (SCO) Perform SCO for: Receptor &nbsp&nbsp&nbsp Ligand
SCO Level:
Backbone Refinement Number of normal modes:
Backbone flexibility level: (range: 0-1)
Rigid-Body Optimization Number of MC Cycles:
Scoring Complex Type:
Atomic radius scale: