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Journal of Computer-Aided Molecular Design

, Volume 30, Issue 9, pp 753–759 | Cite as

Yada: a novel tool for molecular docking calculations

  • S. PiottoEmail author
  • L. Di Biasi
  • R. Fino
  • R. Parisi
  • L. Sessa
  • S. Concilio
Article

Abstract

Molecular docking is a computational method employed to estimate the binding between a small ligand (the drug candidate) and a protein receptor that has become a standard part of workflow in drug discovery. Generally, when the binding site is known and a molecule is similar to known ligands, the most popular docking methods are rather accurate in the prediction of the geometry. Unfortunately, when the binding site is unknown, the blind docking analysis requires large computational resources and the results are often not accurate. Here we present Yada, a new tool for molecular docking that is capable to distribute efficiently calculations onto general purposes computer grid and that combines biological and structural information of the receptor. Yada is available for Windows and Linux and it is free to download at www.yada.unisa.it.

Keywords

Molecular docking Yada Sequence conservation Phylogenetic information 

Notes

Acknowledgments

This work was partially supported by the COST Action CM134 (Emergence and Evaluation of Complex Systems).

Supplementary material

10822_2016_9953_MOESM1_ESM.docx (29 kb)
Supplementary material 1 (DOCX 28 kb)

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

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

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