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BioSolveIT GmbH leadit 2.1.2
Tools and procedures applicable to the in silico/computational antifungal drug repurposing.
Leadit 2.1.2, supplied by BioSolveIT GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/leadit+2%2E1%2E2/leadit+version+2+3+2/pmc07697925-5-102-104
Average 90 stars, based on 1 article reviews
leadit 2.1.2 - by Bioz Stars, 2026-09
90/100 stars

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1) Product Images from "Antifungal Drug Repurposing"

Article Title: Antifungal Drug Repurposing

Journal: Antibiotics

doi: 10.3390/antibiotics9110812

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

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

Related Articles

Software:

Article Title: Design, synthesis, and computational studies on dihydropyrimidine scaffolds as potential lipoxygenase inhibitors and cancer chemopreventive agents
Article Snippet: Molecular Operating Environment (MOE) 2013.08 package license was purchased from Chemical Computing Group Inc (Montreal, QC, Canada), and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH (Sankt Augustin, Germany)., The synthetic strategy employed to produce DHPM1–DHPM8 is illustrated in .

Article Title: Stepwise design, synthesis, and in vitro antifungal screening of ( Z )-substituted-propenoic acid derivatives with potent broad-spectrum antifungal activity
Article Snippet: Molecular Operating Environment (MOE) 2014.09 package license was purchased from Chemical Computing Group Inc, Montreal, QC, Canada and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH, Sankt Augustin, Germany.

Article Title: Synthesis, molecular docking study, and anticancer activity of triaryl-1,2,4-oxadiazole
Article Snippet: This study describes synthesis of a new group of triaryl-1,2,4-oxadiazole derivatives and their anticancer activities.. The target compounds were prepared from reaction of different imines and 4-substituted benzohydroxyiminoyl chlorides.. All the synthesized compounds were screened for antiproliferative activities against MCF7 and K562 cell lines using MTT assay at 50-lM concentration.

Article Title: 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).

Selection:

Article Title: Design, synthesis, and computational studies on dihydropyrimidine scaffolds as potential lipoxygenase inhibitors and cancer chemopreventive agents
Article Snippet: Molecular Operating Environment (MOE) 2013.08 package license was purchased from Chemical Computing Group Inc (Montreal, QC, Canada), and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH (Sankt Augustin, Germany)., The synthetic strategy employed to produce DHPM1–DHPM8 is illustrated in .

Article Title: Stepwise design, synthesis, and in vitro antifungal screening of ( Z )-substituted-propenoic acid derivatives with potent broad-spectrum antifungal activity
Article Snippet: Molecular Operating Environment (MOE) 2014.09 package license was purchased from Chemical Computing Group Inc, Montreal, QC, Canada and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH, Sankt Augustin, Germany.

Article Title: Synthesis, molecular docking study, and anticancer activity of triaryl-1,2,4-oxadiazole
Article Snippet: This study describes synthesis of a new group of triaryl-1,2,4-oxadiazole derivatives and their anticancer activities.. The target compounds were prepared from reaction of different imines and 4-substituted benzohydroxyiminoyl chlorides.. All the synthesized compounds were screened for antiproliferative activities against MCF7 and K562 cell lines using MTT assay at 50-lM concentration.

Article Title: 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).

Biomarker Discovery:

Article Title: Design, synthesis, and computational studies on dihydropyrimidine scaffolds as potential lipoxygenase inhibitors and cancer chemopreventive agents
Article Snippet: Molecular Operating Environment (MOE) 2013.08 package license was purchased from Chemical Computing Group Inc (Montreal, QC, Canada), and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH (Sankt Augustin, Germany)., The synthetic strategy employed to produce DHPM1–DHPM8 is illustrated in .

Article Title: Stepwise design, synthesis, and in vitro antifungal screening of ( Z )-substituted-propenoic acid derivatives with potent broad-spectrum antifungal activity
Article Snippet: Molecular Operating Environment (MOE) 2014.09 package license was purchased from Chemical Computing Group Inc, Montreal, QC, Canada and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH, Sankt Augustin, Germany.

Article Title: Synthesis, molecular docking study, and anticancer activity of triaryl-1,2,4-oxadiazole
Article Snippet: This study describes synthesis of a new group of triaryl-1,2,4-oxadiazole derivatives and their anticancer activities.. The target compounds were prepared from reaction of different imines and 4-substituted benzohydroxyiminoyl chlorides.. All the synthesized compounds were screened for antiproliferative activities against MCF7 and K562 cell lines using MTT assay at 50-lM concentration.

Article Title: 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).

Modification:

Article Title: Design, synthesis, and computational studies on dihydropyrimidine scaffolds as potential lipoxygenase inhibitors and cancer chemopreventive agents
Article Snippet: Molecular Operating Environment (MOE) 2013.08 package license was purchased from Chemical Computing Group Inc (Montreal, QC, Canada), and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH (Sankt Augustin, Germany)., The synthetic strategy employed to produce DHPM1–DHPM8 is illustrated in .

Article Title: Stepwise design, synthesis, and in vitro antifungal screening of ( Z )-substituted-propenoic acid derivatives with potent broad-spectrum antifungal activity
Article Snippet: Molecular Operating Environment (MOE) 2014.09 package license was purchased from Chemical Computing Group Inc, Montreal, QC, Canada and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH, Sankt Augustin, Germany.

Article Title: Synthesis, molecular docking study, and anticancer activity of triaryl-1,2,4-oxadiazole
Article Snippet: This study describes synthesis of a new group of triaryl-1,2,4-oxadiazole derivatives and their anticancer activities.. The target compounds were prepared from reaction of different imines and 4-substituted benzohydroxyiminoyl chlorides.. All the synthesized compounds were screened for antiproliferative activities against MCF7 and K562 cell lines using MTT assay at 50-lM concentration.

Article Title: 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).

Bioassay:

Article Title: Design, synthesis, and computational studies on dihydropyrimidine scaffolds as potential lipoxygenase inhibitors and cancer chemopreventive agents
Article Snippet: Molecular Operating Environment (MOE) 2013.08 package license was purchased from Chemical Computing Group Inc (Montreal, QC, Canada), and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH (Sankt Augustin, Germany)., The synthetic strategy employed to produce DHPM1–DHPM8 is illustrated in .

Article Title: Stepwise design, synthesis, and in vitro antifungal screening of ( Z )-substituted-propenoic acid derivatives with potent broad-spectrum antifungal activity
Article Snippet: Molecular Operating Environment (MOE) 2014.09 package license was purchased from Chemical Computing Group Inc, Montreal, QC, Canada and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH, Sankt Augustin, Germany.

Article Title: Synthesis, molecular docking study, and anticancer activity of triaryl-1,2,4-oxadiazole
Article Snippet: This study describes synthesis of a new group of triaryl-1,2,4-oxadiazole derivatives and their anticancer activities.. The target compounds were prepared from reaction of different imines and 4-substituted benzohydroxyiminoyl chlorides.. All the synthesized compounds were screened for antiproliferative activities against MCF7 and K562 cell lines using MTT assay at 50-lM concentration.

Article Title: 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).

MTT Microdilution Assay:

Article Title: Design, synthesis, and computational studies on dihydropyrimidine scaffolds as potential lipoxygenase inhibitors and cancer chemopreventive agents
Article Snippet: Molecular Operating Environment (MOE) 2013.08 package license was purchased from Chemical Computing Group Inc (Montreal, QC, Canada), and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH (Sankt Augustin, Germany)., The synthetic strategy employed to produce DHPM1–DHPM8 is illustrated in .

Article Title: Stepwise design, synthesis, and in vitro antifungal screening of ( Z )-substituted-propenoic acid derivatives with potent broad-spectrum antifungal activity
Article Snippet: Molecular Operating Environment (MOE) 2014.09 package license was purchased from Chemical Computing Group Inc, Montreal, QC, Canada and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH, Sankt Augustin, Germany.

Article Title: Synthesis, molecular docking study, and anticancer activity of triaryl-1,2,4-oxadiazole
Article Snippet: This study describes synthesis of a new group of triaryl-1,2,4-oxadiazole derivatives and their anticancer activities.. The target compounds were prepared from reaction of different imines and 4-substituted benzohydroxyiminoyl chlorides.. All the synthesized compounds were screened for antiproliferative activities against MCF7 and K562 cell lines using MTT assay at 50-lM concentration.

Article Title: 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).

Binding Assay:

Article Title: Design, synthesis, and computational studies on dihydropyrimidine scaffolds as potential lipoxygenase inhibitors and cancer chemopreventive agents
Article Snippet: Molecular Operating Environment (MOE) 2013.08 package license was purchased from Chemical Computing Group Inc (Montreal, QC, Canada), and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH (Sankt Augustin, Germany)., The synthetic strategy employed to produce DHPM1–DHPM8 is illustrated in .

Article Title: Stepwise design, synthesis, and in vitro antifungal screening of ( Z )-substituted-propenoic acid derivatives with potent broad-spectrum antifungal activity
Article Snippet: Molecular Operating Environment (MOE) 2014.09 package license was purchased from Chemical Computing Group Inc, Montreal, QC, Canada and Leadit 2.1.2 software license was purchased from BioSolveIT GmbH, Sankt Augustin, Germany.

Article Title: Synthesis, molecular docking study, and anticancer activity of triaryl-1,2,4-oxadiazole
Article Snippet: This study describes synthesis of a new group of triaryl-1,2,4-oxadiazole derivatives and their anticancer activities.. The target compounds were prepared from reaction of different imines and 4-substituted benzohydroxyiminoyl chlorides.. All the synthesized compounds were screened for antiproliferative activities against MCF7 and K562 cell lines using MTT assay at 50-lM concentration.

Article Title: 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).



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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