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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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You can supply Rosetta with simulation constraints. A constraint file is a text file with the format:
Constraint_Type1 Constraint_Def1Constraint_Type2 Constraint_Def2...
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.
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.
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