FlexPepDock is a high-resolution peptide-protein docking (refinement) protocol for the modeling of peptide-protein complexes, implemented in the Rosetta framework.
For more details see the "Overview" and "Usage & FAQ" sections.
You can supply Rosetta with simulation constraints. A constraint file is a text file with the format:
Note that you can apply contraints only on high-resolution runs.
You can find more information about constraint files here
A reference file is a PDB file that contains both the peptide and the protein.
RMS calculated by rosetta will be measured against this structure rather than the structure submitted for the FlexPepDock run.
Giving your job a name helps to distinguish between multiple jobs being submitted.
By default, the job is given the same name as the submitted file.
Checking this will place a link to your submission and its FlexPepDock results for other users of the server to view and use. Shared jobs get higher priority.
Customize number of structures
FlexPepDock returns by default results from a 100 high-resolution simulations and a 100 low-resolution simulations. You can customize the number of simulations from each type up to 300. If either of the fields remains blank 100 structures will be simulated by default.
Note that low-resolution runs cannot handle phosphorylation, so if you have phosphate atoms in your structure set the number of low-resolution structures to 0. Don't forget the tag these atoms with ATOM rather than HETATM as FlexPepDock ignores all non-ATOM entries.
E-mail addresses submitted to FlexPepDock's web
server are only used for tracking user's usage and returning
analysis results. We may also contact you via email should any
problem arise with you submission. Be sure that email addresses are
not used for any other purpose and are not passed to third parties.
Intellectual Property Disclaimer
All data submitted to FlexPepDock's web server
and it's analysis results is publicly accessible, hence we cannot