GlycopeptideDockingProtocol.cc File Reference

A protocol to predict glycopeptide_docking and elongation of glycans on peptide/glycopeptide, lipid and protein substrates by glycosyltransferase. Current implementation only includes glycosylation of peptides and glycopeptides. It has been tested on GalNAcT2-peptide and GalNAcT12-glypeptide systems to predict peptide substrate specificity(T2) and di-glycopeptide binding sites(T12). Also, limited testing on N-linked glycosylation by enzyme ApNGT. More...

#include <protocols/glycopeptide_docking/GlycopeptideDockingProtocol.hh>
#include <protocols/glycopeptide_docking/GlycopeptideDockingProtocolCreator.hh>
#include <protocols/glycopeptide_docking/GlycopeptideDockingFlags.hh>
#include <protocols/glycopeptide_docking/GlycopeptideDockingHighResRefinement.hh>
#include <protocols/glycopeptide_docking/GlycopeptideDockingLowResRefinement.hh>
#include <protocols/glycopeptide_docking/utils.hh>
#include <protocols/carbohydrates/SimpleGlycosylateMover.hh>
#include <protocols/carbohydrates/GlycanSampler.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/constraint_movers/ConstraintSetMover.hh>
#include <protocols/docking/util.hh>
#include <protocols/docking/metrics.hh>
#include <protocols/jd2/Job.hh>
#include <protocols/jd2/JobDistributor.hh>
#include <core/pose/Pose.hh>
#include <core/types.hh>
#include <core/kinematics/Edge.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/ScoreType.hh>
#include <core/import_pose/import_pose.hh>
#include <core/conformation/Residue.hh>
#include <core/select/residue_selector/ResidueIndexSelector.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <basic/Tracer.hh>
#include <utility/tag/Tag.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/vector1.hh>
#include <utility/excn/Exceptions.hh>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/run.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <numeric/random/random.hh>
#include <numeric/xyzVector.hh>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <protocols/moves/mover_schemas.hh>
#include <string>
#include <list>
#include <map>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::glycopeptide_docking

Functions
static basic::Tracer	TR ("protocols.glycopeptide_docking.GlycopeptideDockingProtocol")
std::ostream &	protocols::glycopeptide_docking::operator<< (std::ostream &os, GlycopeptideDockingProtocol const &mover)

Detailed Description

A protocol to predict glycopeptide_docking and elongation of glycans on peptide/glycopeptide, lipid and protein substrates by glycosyltransferase. Current implementation only includes glycosylation of peptides and glycopeptides. It has been tested on GalNAcT2-peptide and GalNAcT12-glypeptide systems to predict peptide substrate specificity(T2) and di-glycopeptide binding sites(T12). Also, limited testing on N-linked glycosylation by enzyme ApNGT.

Author

Yashes Srinivasan (yashe.nosp@m.ss@g.nosp@m.mail..nosp@m.com), Sai Pooja Mahajan (saipo.nosp@m.oja@.nosp@m.gmail.nosp@m..com)

Function Documentation

static basic::Tracer TR ( "protocols.glycopeptide_docking.GlycopeptideDockingProtocol"  )

static