FlexPepDock

Rosetta FlexPepDock is a high-resolution peptide docking (refinement) protocol, implemented within the Rosetta framework. The input for this server is a PDB file of a complex between a protein receptor (first chain) and an estimated conformation for a peptide (second chain). FlexPepDock was shown to be able to accurately refine the peptide structure starting from up to 5.5A RMSD of the native conformation, allowing full flexibility to the peptide and side-chain flexibility to the receptor.

For more details see the "Overview" and "Usage & FAQ" sections.
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Recently shared jobs: 1abc_abcl33b.pdb Peptide#3.pdb Peptide_3.pdb 1M60, pep-F 3upr w/ pep-v backbone 3upr_test w/ pep-v backbone 3UPR.pdb B5701 w/ peptide V fXIIa-subs.000.02.pdb flex_dock_1QRQ_PIF_fix.pdb



Input PDB file:

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Advanced Options (click to toggle)

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Insert a reference PDB Learn more

Insert a constraint file Learn more

Specify number of low resolution structures (0-300)

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Specify number of high resolution structures (0-300)

Select columns to appear in data file:

score hbond_sc rama I_sc pep_sc
rmsBB_if fa_atr fa_pair pep_sc_noref rmsALL_if
fa_rep fa_dun rmsBB fa_sol startRMSbb

Constraint file

You can supply Rosetta with simulation constraints. A constraint file is a text file with the format:

Constraint_Type1 Constraint_Def1
Constraint_Type2 Constraint_Def2...

Note that you can apply contraints only on high-resolution runs.

You can find more information about constraint files here

Reference file

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.

Job name

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.

Share job

Checking this will place a link to your submission and its FlexPepDock results for other users of the server to view and use.

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.




Data Protection

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 guarantee confidentiality.