A New Flexible Protocol for Docking Studies

  • Lucia SessaEmail author
  • Luigi Di Biasi
  • Simona Concilio
  • Giuseppe Cattaneo
  • Alfredo De Santis
  • Pio Iannelli
  • Stefano Piotto
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 587)


A significant prerequisite for computational structure-based drug design is the estimation of the structures of ligand-receptor complexes. For this task, the flexibility of both ligand and receptor backbone is required, but it requires the exploration of an extremely vast conformational space. Here we present a protocol to address the receptor flexibility using complementary strategies and the use of receptor sequence conservation. The method aims to increase the accuracy of predicted ligand orientation in the binding pocket and the receptor-ligand binding affinity. The precision in affinity prediction permits to distinguish between binders and non-binders and to identify binding sites and ligand poses necessary for lead optimization.


Androgen Receptor Binding Pocket Root Mean Square Deviation Internal Cavity Receptor Structure 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work was partially supported by the “Data-Driven Genomic Computing (GenData 2020)” PRIN project (2013–2015), funded by the Italian Ministry of the University and Research (MIUR).


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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Lucia Sessa
    • 1
    Email author
  • Luigi Di Biasi
    • 1
    • 2
  • Simona Concilio
    • 3
  • Giuseppe Cattaneo
    • 2
  • Alfredo De Santis
    • 2
  • Pio Iannelli
    • 1
  • Stefano Piotto
    • 1
  1. 1.Department of PharmacyUniversity of SalernoFiscianoItaly
  2. 2.Department of InformaticsUniversity of SalernoFiscianoItaly
  3. 3.Department of Industrial EngineeringUniversity of SalernoFiscianoItaly

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