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J Comput Aided Mol Des. 2016 Sep;30(9):753-759. Epub 2016 Aug 26.

Yada: a novel tool for molecular docking calculations.

Author information

1
Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy. piotto@unisa.it.
2
Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
3
Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.

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; Phylogenetic information; Sequence conservation; Yada

PMID:
27565794
DOI:
10.1007/s10822-016-9953-9
[Indexed for MEDLINE]

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