Journal of Computer-Aided Molecular Design

, Volume 30, Issue 9, pp 773–789

DockBench as docking selector tool: the lesson learned from D3R Grand Challenge 2015

  • Veronica Salmaso
  • Mattia Sturlese
  • Alberto Cuzzolin
  • Stefano Moro

DOI: 10.1007/s10822-016-9966-4

Cite this article as:
Salmaso, V., Sturlese, M., Cuzzolin, A. et al. J Comput Aided Mol Des (2016) 30: 773. doi:10.1007/s10822-016-9966-4


Structure-based drug design (SBDD) has matured within the last two decades as a valuable tool for the optimization of low molecular weight lead compounds to highly potent drugs. The key step in SBDD requires knowledge of the three-dimensional structure of the target-ligand complex, which is usually determined by X-ray crystallography. In the absence of structural information for the complex, SBDD relies on the generation of plausible molecular docking models. However, molecular docking protocols suffer from inaccuracies in the description of the interaction energies between the ligand and the target molecule, and often fail in the prediction of the correct binding mode. In this context, the appropriate selection of the most accurate docking protocol is absolutely relevant for the final molecular docking result, even if addressing this point is absolutely not a trivial task. D3R Grand Challenge 2015 has represented a precious opportunity to test the performance of DockBench, an integrate informatics platform to automatically compare RMDS-based molecular docking performances of different docking/scoring methods. The overall performance resulted in the blind prediction are encouraging in particular for the pose prediction task, in which several complex were predicted with a sufficient accuracy for medicinal chemistry purposes.


DockBench D3R Grand Challenge 2015 Blind prediction Molecular docking Docking benchmark 

Supplementary material

10822_2016_9966_MOESM1_ESM.docx (828 kb)
Supplementary material 1 (DOCX 827 kb)

Funding information

Funder NameGrant NumberFunding Note
Università degli Studi di Padova
  • Progetto Giovani Studiosi 2013: Protocol number 79122

Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaPaduaItaly

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