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Tools and procedures applicable to the in silico/computational antifungal drug repurposing.

Journal: Antibiotics

Article Title: Antifungal Drug Repurposing

doi: 10.3390/antibiotics9110812

Figure Lengend Snippet: Tools and procedures applicable to the in silico/computational antifungal drug repurposing.

Article Snippet: Ligand preparation and Molecular docking , OMEGA v.3.0.0.1 software by OpenEye Scientific [ ]; QUACPAC v.1.7.0.2 software by OpenEye Scientific [ ]; OEDocking suite v.3.2.0 by OpenEye Scientific [ ]; FRED program with the ChemGauss4 score function in the OEDocking suite , Protein Preparation Wizard of Schrodinger’s suite 8.5 (Chimeric 1EA1); Docking between internal ligand (fluconazole) and 1EA1 in Schrodinger’s suite 8.5; GROMACS 5.0 for molecular dynamics simulations with GROMOS9643a1 force field; LIGPREP and MAESTRO (fluvastatin 3D structure); MATLAB version R2015b (plotting and calculations); Dundee Prodrug 2.5; GLIDE 5.0 , MOE 2014.09 (Chemical Computing Group Inc., Sherbooke St, Montreal, QC, Canada) software; Leadit 2.1.2 (BioSolveIT GmbH, Germany) software; Gromacs 4.5.5 (Molecular dynamics); PRODRG2 and GROMOS 53A6 force field (Topology); Particle Mesh Ewald (PME) method and linear constraint solver (LINCS); Xmgrace and VMD software , AutoDock Vina program; PyRx suite open-source software version 0.9.7; AutoDock Vina program; Discovery Studio Visualizer version 17.2.0 (Dassault Systemes Biovia Corp.) , Scaffold Hunter program ( http://scaffoldhunter.sourceforge.net/ ) (selection of top ten best compounds from each database); GOLD software (docking simulation against Candida albicans thioredoxin reductase); CORINA (three-dimensional models); Visual Molecular Dynamics (VMD) program ( http://www.ks.uiuc.edu/Research/vmd/ ); LigPlot program ( https://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/ ) , Protein preparation wizard ( C. albicans CYP51 ); LigPrep module of the Schrodinger suite (sertraline); Schrodinger suite (LLC, New York, NY) (induced fit molecular docking analysis); Glide module (extra precision feature for sertraline).

Techniques: Biomarker Discovery, Selection, Software, Modification, Bioassay, MTT Microdilution Assay