Motivation: Root mean square deviation (RMSD) is one of the most useful and straightforward features for structural comparison between different conformations of the same molecule. Commonly, protein-ligand docking programs have included some utilities that allow the calculation of this value; however, they only work efficiently when exists a complete atom label equivalence between the evaluated conformations.
Results: We present LigRMSD, a free web-server for the automatic matching and RMSD calculations among identical or similar chemical compounds. This server allows the user to submit only a pair of identical or similar molecules or dataset of similar compounds to compare their three-dimensional conformations.
Availability and implementation: LigRMSD can be freely accessed at https://ligrmsd.appsbio.utalca.cl.
Supplementary information: Supplementary data are available at Bioinformatics online.
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