The scripts and input files that accompany this demo can be found in the
demos/public directory of the Rosetta weekly releases.
KEYWORDS: DOCKING INTERFACES
In this demo, a peptide (chain B) is docked onto a protein (chain A) with user-defined constraints. The purpose of this demo is to illustrate the use of constraint files and as many different types of constraints as possible. The input files are based on PDB ID (2o2m) which is a "Crystal Structure Of Human Gαi1 Bound To The Goloco Motif Of Rgs14". The protein is chain A. The peptide is chain B.
A general overview of the protocol is available at:
A write-up of the file format for Constraints is available at:
High level overview:
Docking with constraints. In general, constraints are typically defined for CA atoms of the partner sidechains.
A good overview of constraints is available in the documentation:
The three constraints which are honored by the Docking Protocol are:
AtomPair and AmbiguousConstraint are described the above documentation for Rosetta 3.2.1. A SiteConstraint allows you to specify that a particular residue should be in contact with a particular chain. An example of a SiteConstraint is:
SiteConstraint CA 4A D FLAT_HARMONIC 0 1 5
This will add a FLAT_HARMONIC potential with the parameters 0 1 5 (recommended) around the distance between the CA of residue 4 (PDB numbering) on chain A and the closest CA on chain D to the ScoreFunction.
To run these examples, use
$> <path/to/Rosetta/main/source/bin/>/docking_protocol.default.linuxgccrelease @rosetta_inputs/options $> <path/to/Rosetta/main/source/bin/>/docking_protocol.default.linuxgccrelease @rosetta_inputs/options.constraint_ambiguous $> <path/to/Rosetta/main/source/bin/>/docking_protocol.default.linuxgccrelease @rosetta_inputs/options_wo_constraints