Modelling covalent linkages in CCP4

The mechanism for modelling covalent linkages in CCP4 is reviewed and the method of link-dictionary generation used by AceDRG is described. An overview of the various protocols available for the modelling and application of covalent linkages within the CCP4 suite is presented, providing instructive guidelines with a focus on practical application.

The missing link: covalent linkages in structural models

Analysis of the Protein Data Bank revealed that over a third of entries contain covalent linkages without descriptions in the CCP4 Monomer Library (CCP4-ML). The CCP4-ML was updated with AceDRG dictionaries corresponding to commonly occurring classes of missing linkages.