title: Tools for ligand validation in Coot.
abstract: Coot is a molecular-graphics program primarily aimed at model building using X-ray data. Recently, tools for the manipulation and representation of ligands have been introduced. Here, these new tools for ligand validation and comparison are described. Ligands in the wwPDB have been scored by density-fit, distortion and atom-clash metrics. The distributions of these scores can be used to assess the relative merits of the particular ligand in the protein-ligand complex of interest by means of `sliders' akin to those now available for each accession code on the wwPDB websites.
authors.affiliation: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England.
authors.forename: Paul
authors.initials: P
authors.lastname: Emsley
mesh_terms: D001665:Binding Sites; D003196:Computer Graphics; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D008024:Ligands; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D054852:Small Molecule Libraries / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins; D054852:Small Molecule Libraries
keywords: Coot; ligand manipulation; ligand representation; ligand validation; model building