Open3DALIGN: an open-source software aimed at unsupervised ligand alignment

  • Paolo Tosco
  • Thomas Balle
  • Fereshteh Shiri


An open-source, cross-platform software aimed at conformer generation and unsupervised rigid-body molecular alignment is presented. Different algorithms have been implemented to perform single and multi-conformation superimpositions on one or more templates. Alignments can be accomplished by matching pharmacophores, heavy atoms or a combination of the two. All methods have been successfully validated on eight comprehensive datasets previously gathered by Sutherland and co-workers. High computational performance has been attained through efficient parallelization of the code. The unsupervised nature of the alignment algorithms, together with its scriptable interface, make Open3DALIGN an ideal component of high-throughput, automated cheminformatics workflows.


Cheminformatics Alignment Superposition Pharmacophore 



We are grateful to the developers of OpenBabel, Pharao and TINKER, on which Open3DALIGN depends to do its job, and to an anonymous reviewer who contributed to improve this manuscript. We acknowledge the support of Chemical Computing Group. Part of this work was carried out by P.T. at the University of Copenhagen under a visiting scientist grant supported by the Drug Research Academy (DRA). T.B. was supported by grants from the Lundbeck Foundation. Part of this work was carried out by F.S. at the University of Turin under a visiting scientist grant.


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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Department of Drug Science and TechnologyUniversity of TurinTurinItaly
  2. 2.Department of Medicinal ChemistryThe Faculty of Pharmaceutical Sciences, University of CopenhagenCopenhagenDenmark
  3. 3.Faculty of ChemistryRazi UniversityKermanshahIran

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