title: Yada: a novel tool for molecular docking calculations.
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 .
authors: Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy. piotto@unisa.it.
authors: S
authors: 0000-0002-3102-1918
authors: S
authors: Piotto
authors: Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
authors: L
authors: L
authors: Di Biasi
authors: Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
authors: R
authors: R
authors: Fino
authors: Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
authors: R
authors: R
authors: Parisi
authors: Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
authors: L
authors: L
authors: Sessa
authors: Department of Industrial Engineering, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
authors: S
authors: S
authors: Concilio
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D055808:Drug Discovery / Q000379:methods; D005982:Glutathione Transferase / Q000737:chemistry; D008024:Ligands; D062105:Molecular Docking Simulation / Q000379:methods*; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D008024:Ligands; D005982:Glutathione Transferase
keywords: Molecular docking; Phylogenetic information; Sequence conservation; Yada