LigRMSD: a web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking
José Luís Velázquez‐Libera, Fabio Durán-Verdugo, Alejandro Valdés-Jiménez, Gabriel Núñez, Julio Caballero
Abstract
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.