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Fragment Based Molecular Dynamics for Drug Design

  • Lucia Sessa
  • Luigi Di Biasi
  • Simona Concilio
  • Stefano Piotto
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 830)

Abstract

Molecular docking is a computationally efficient method used to predict the conformations adopted by the ligand within a target-binding site. A positive aspect of conventional docking is the possibility of easily distributing the calculation on dedicated grid or cluster. The receptor is usually kept rigid, therefore the changes in the binding pocket geometry induced by the ligand is overlooked. Here we present a new docking approach (DynDock) that exploits molecular dynamics to preserve the flexibility of the receptor. To maintain high computational efficiency, DynDock has been developed to be distributed on a grid. The main advantages of this method are the full flexible molecular docking achieved during the simulation and the reduced number of compounds collected.

Keywords

Docking Drug design Molecular dynamics 

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of PharmacyUniversity of SalernoFiscianoItaly
  2. 2.Department of Industrial EngineeringUniversity of SalernoFiscianoItaly

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