Directory dependency graph for glycopeptide_docking:
Files | |
| file | GlycopeptideDockingFlags.cc |
| Holds flags, options, and pose variables for the Glycosylation Protocol. | |
| file | GlycopeptideDockingFlags.fwd.hh |
| Holds flags, options, and pose variables for the Glycosylation Protocol. | |
| file | GlycopeptideDockingFlags.hh |
| file | GlycopeptideDockingHighResRefinement.cc |
| file | GlycopeptideDockingHighResRefinement.fwd.hh |
| High resolution refinement of glycosyltransferase substrate. | |
| file | GlycopeptideDockingHighResRefinement.hh |
| High resolution refinement of glycosyltransferase peptide/glycopeptide substrate complex. This protocol applies MCM sampling in torsional and rigid body space with sidechain repacking of the substrate and substrate-enzyme interface. The attractive and repulsive terms are ramped down and up respectively to allow softer potential at the beginning of the run. Protocol similar to high resolution refinement of flexpepdock. | |
| file | GlycopeptideDockingLowResRefinement.cc |
| file | GlycopeptideDockingLowResRefinement.fwd.hh |
| Low resolution refinement of substrate. | |
| file | GlycopeptideDockingLowResRefinement.hh |
| Low resolution refinement of substrate. | |
| file | GlycopeptideDockingProtocol.cc |
| 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. | |
| file | GlycopeptideDockingProtocol.fwd.hh |
| A protocol to predict glycopeptide_docking and elongation of glycans. | |
| file | GlycopeptideDockingProtocol.hh |
| A protocol to dock peptide or glycosylate peptide in the glycopeptide_docking site of a glycosyltransferase. The protocol is designed for O-linked glycopeptide_docking in which sugar are transferred one-at-a-time by specific glycosytransferases to a peptide (or glycopeptide) or protein substrate from a nucleatide donor (eg. UDP-GalNAc) The current version of the protocol has been tested on GalNAcT transferases that add the first sugar in the O-linked pathway. The protocol is in active development for extension to other enzymes in the O-glycopeptide_docking pathway. Currently, the protocol requires the pose to contain the enzyme, activated sugar (or just UDP), and a peptide substrate. | |
| file | GlycopeptideDockingProtocolCreator.hh |
| A protocol to predict glycopeptide_docking and elongation of glycans. | |
| file | utils.cc |
| util functions for peptide/glycopeptide sampling and refinement | |
| file | utils.hh |
