MetalInterfaceStructureCreator.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/metal_interface/MetalInterfaceDesignMover.hh>
#include <apps/pilot/rjha/MetalInterface.hh>
#include <core/pose/Pose.hh>
#include <core/pose/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 <devel/init.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <string>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/import_pose/import_pose.hh>

Namespaces
	devel
	devel::metal_interface

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

Variables
static basic::Tracer	TR ("apps.pilot.rjha")
basic::options::FileOptionKey const	devel::metal_interface::partner1 ("MetalInterface::partner1")
basic::options::FileOptionKey const	devel::metal_interface::partner2 ("MetalInterface::partner2")
basic::options::FileOptionKey const	devel::metal_interface::match ("MetalInterface::match")
basic::options::IntegerOptionKey const	devel::metal_interface::partner2_residue ("MetalInterface::partner2_residue")
basic::options::BooleanOptionKey const	devel::metal_interface::skip_sitegraft_repack ("MetalInterface::skip_sitegraft_repack")
basic::options::BooleanOptionKey const	devel::metal_interface::RMS_mode ("MetalInterface::RMS_mode")

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 and Ramesh Jha

Function Documentation

main()

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

References argv, utility::file::FileName::base(), predPRE::chain, build_jacobian::distance, test.T009_Exceptions::e, find_closest_atom(), create_a3b_hbs::i, basic::init(), devel::metal_interface::match, metal, utility::file::FileName::name(), basic::options::OptionKeys::in::file::native, lactamize::new_name, basic::options::option, option, p1_1, p2, vancomycin::pack, devel::metal_interface::partner1, devel::metal_interface::partner2, devel::metal_interface::partner2_residue, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::residue_type_set, devel::metal_interface::RMS_mode, basic::options::OptionKeys::in::file::s, beta_nonlocal::score_fxn, devel::metal_interface::skip_sitegraft_repack, vancomycin::task, TR, utility_exit_with_message, and value.

Variable Documentation

TR

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

static

Referenced by main().