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Coot is a molecular-graphics application primarily aimed to assist in model building and validation of biological macromolecules. Recently, tools have been added to work with small molecules. The newly incorporated tools for the manipulation and validation of ligands include interaction with PRODRG, subgraph isomorphism-based tools, representation of ligand chemistry, ligand fitting and analysis, and are described here.doi:10.1107/s0907444912000200 pmid:22505262 pmcid:PMC3322601 fatcat:vb6ceevxnjadhprv74tpxmqdta