Rosetta  2020.46
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Namespaces | Enumerations | Functions | Variables
zinc_heterodimer_design.cc File Reference

This is the application for a metal interface design project. In its initial conception, the idea was to design an interface between ankyrin and ubc12. First, RosettaMatch is used to design a histidine/cystine zinc binding site on ankyrin (3 residues). The fourth residue to coordinate a tetrahedral zinc then comes from ubc12 (present natively). This metal binding gets the interface going; the protocol searches rigid-body space to try to find a shape-complementary interaction and then designs the interface. More...

#include <devel/init.hh>
#include <protocols/metal_interface/FindClosestAtom.hh>
#include <protocols/metal_interface/ZincHeterodimerMover.hh>
#include <core/pose/Pose.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/pose/PDBPoseMap.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/PackerTask.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/Stub.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ChemicalManager.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <utility/file/FileName.hh>
#include <numeric/xyzVector.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <string>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>

Namespaces

 local
 

Enumerations

enum  MatchPosition {
  p1_1 = 1, p1_2 = 2, p1_3 = 3, p2 = 4,
  metal = 5
}
 

Functions

int main (int argc, char *argv[])
 

Variables

static basic::Tracer TR ("apps.pilot.rjha")
 
basic::options::FileOptionKey const local::partner1 ("partner1")
 
basic::options::FileOptionKey const local::partner2 ("partner2")
 
basic::options::FileOptionKey const local::match_pdb ("match_pdb")
 
basic::options::IntegerOptionKey
const 
local::partner2_residue ("partner2_residue")
 
basic::options::BooleanOptionKey
const 
local::skip_sitegraft_repack ("skip_sitegraft_repack")
 

Detailed Description

This is the application for a metal interface design project. In its initial conception, the idea was to design an interface between ankyrin and ubc12. First, RosettaMatch is used to design a histidine/cystine zinc binding site on ankyrin (3 residues). The fourth residue to coordinate a tetrahedral zinc then comes from ubc12 (present natively). This metal binding gets the interface going; the protocol searches rigid-body space to try to find a shape-complementary interaction and then designs the interface.

Author
Steven Lewis, Ramesh Jha, Bryan Der

Enumeration Type Documentation

Enumerator
p1_1 
p1_2 
p1_3 
p2 
metal 

Function Documentation

int main ( int  argc,
char *  argv[] 
)

Variable Documentation

basic::Tracer TR("apps.pilot.rjha")
static

Referenced by main().