LigRMSD: a web server for automatic structure matching and RMSD calculations among identical and similar compounds in protein-ligand docking

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...

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Published inBioinformatics Vol. 36; no. 9; pp. 2912 - 2914
Main Authors Velázquez-Libera, José Luis, Durán-Verdugo, Fabio, Valdés-Jiménez, Alejandro, Núñez-Vivanco, Gabriel, Caballero, Julio
Format Journal Article
LanguageEnglish
Published England Oxford University Press 01.05.2020
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Summary: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.
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ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btaa018