Automated ligand fitting by core-fragment fitting and extension into density

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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, background): “(iii) Ligand identification (phenix.ligand_identification) analyzes difference density peaks to reveal which ligand is likely to be present (Terwilliger et al., 2006, 2007).”
Features and development of Coot (2010, neutral): “Above a certain number of rotatable bonds it is more efﬁcient to use a ‘core + fragment by fragment’ approach (see, for example, Terwilliger et al. , 2006).”
The Phenix Software for Automated Determination of Macromolecular Structures (2011, methodology): “The current Phenix release (1.7) includes GUIs for phenix.refine [22], phenix.xtriage , the AutoSol[27], AutoBuild[23], AutoMR, and LigandFit[28, 29] wizards, Phaser[6], eLBOW[30], the restraints editor REEL, validation tools, and utilities for creating and manipulating maps and reflection files.”
Ligand placement based on prior structures: the guided ligand-replacement method (2013, methodology): “Within Phenix (Adams et al., 2002, 2010), the LigandFit module (Terwilliger et al., 2006) was developed for de novo ligand fitting.”