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/util.hh>
#include <core/pose/init_id_map.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/conformation/Conformation.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.fwd.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ChemicalManager.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <utility/file/FileName.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>
#include <core/pack/task/ResidueLevelTask.hh>

Namespaces
	local

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

MatchPosition

enum MatchPosition

Enumerator
p1_1
p1_2
p1_3
p2
metal
p1_1
p1_2
p1_3
p2
metal

Function Documentation

main()

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

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

Variable Documentation

TR

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

static

Referenced by main().