Molecular modelling tools are used to create and modify the 3D structures of molecules. When experimental structural data is missing, they can be used to predict the structures of biomolecules, biomolecular complexes and of complexes formed between biomolecules and small molecules. They are also used to prepare existing structures for use in simulations, for example, by adding missing side-chains and hydrogen atoms.
Image from: di Luccio E, Koehl P (2011) A quality metric for homology modeling: the H-factor. BMC Bioinformatics 12: 48. doi:10.1186/1471-2105-12-48