期刊
JOURNAL OF CHEMINFORMATICS
卷 12, 期 1, 页码 -出版社
BMC
DOI: 10.1186/s13321-020-00455-2
关键词
RMSD; Symmetry; Software; Python
类别
资金
- Biotechnology and Biological Sciences Research Council (BBSRC) National Productivity Investment Fund (NPIF) [BB/MO11224/1, BB/S50760X/1]
- Evotec (UK) via the Interdisciplinary Biosciences DTP at the University of Oxford
- BBSRC [2108092] Funding Source: UKRI
Root mean square displacement (RMSD) calculations play a fundamental role in the comparison of different conformers of the same ligand. This is particularly important in the evaluation of protein-ligand docking, where different ligand poses are generated by docking software and their quality is usually assessed by RMSD calculations. Unfortunately, many RMSD calculation tools do not take into account the symmetry of the molecule, remain difficult to integrate flawlessly in cheminformatics and machine learning pipelines-which are often written in Python-or are shipped within large code bases. Here we present a new open-source RMSD calculation tool written in Python, designed to be extremely lightweight and easy to integrate into existing software.
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