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

Velazquez-Libera, Jose Luis; Duran-Verdugo, Fabio; Valdes-Jimenez, Alejandro; Nunez-Vivanco, Gabriel; Caballero, Julio

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.

Más información

Título según WOS: ID WOS:000537450900038 Not found in local WOS DB
Título de la Revista: BIOINFORMATICS
Volumen: 36
Número: 9
Editorial: OXFORD UNIV PRESS
Fecha de publicación: 2020
Página de inicio: 2912
Página final: 2914
DOI:

10.1093/bioinformatics/btaa018

Notas: ISI