Journal of Computer-Aided Molecular Design

, Volume 24, Issue 8, pp 675-686

First online:

Open Access This content is freely available online to anyone, anywhere at any time.

Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble

  • Austin B. YongyeAffiliated withTorrey Pines Institute for Molecular Studies
  • , Andreas BenderAffiliated withMedicinal Chemistry Division and Pharma-IT Platform, Leiden/Amsterdam Center for Drug Research, Leiden UniversityUnilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge
  • , Karina Martínez-MayorgaAffiliated withTorrey Pines Institute for Molecular Studies Email author 


Representing the 3D structures of ligands in virtual screenings via multi-conformer ensembles can be computationally intensive, especially for compounds with a large number of rotatable bonds. Thus, reducing the size of multi-conformer databases and the number of query conformers, while simultaneously reproducing the bioactive conformer with good accuracy, is of crucial interest. While clustering and RMSD filtering methods are employed in existing conformer generators, the novelty of this work is the inclusion of a clustering scheme (NMRCLUST) that does not require a user-defined cut-off value. This algorithm simultaneously optimizes the number and the average spread of the clusters. Here we describe and test four inter-dependent approaches for selecting computer-generated conformers, namely: OMEGA, NMRCLUST, RMS filtering and averaged-RMS filtering. The bioactive conformations of 65 selected ligands were extracted from the corresponding protein:ligand complexes from the Protein Data Bank, including eight ligands that adopted dissimilar bound conformations within different receptors. We show that NMRCLUST can be employed to further filter OMEGA-generated conformers while maintaining biological relevance of the ensemble. It was observed that NMRCLUST (containing on average 10 times fewer conformers per compound) performed nearly as well as OMEGA, and both outperformed RMS filtering and averaged-RMS filtering in terms of identifying the bioactive conformations with excellent and good matches (0.5 < RMSD < 1.0 Å). Furthermore, we propose thresholds for OMEGA root-mean square filtering depending on the number of rotors in a compound: 0.8, 1.0 and 1.4 for structures with low (1–4), medium (5–9) and high (10–15) numbers of rotatable bonds, respectively. The protocol employed is general and can be applied to reduce the number of conformers in multi-conformer compound collections and alleviate the complexity of downstream data processing in virtual screening experiments.


Ligand-based drug design Query conformers 3D similarity search Virtual screening Conformer clustering