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A Comparative Study for the Accuracy of Three Molecular Docking Programs Using HIV-1 Protease Inhibitors as a Model
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Flexible molecular docking is a computational method of structure-based drug design to evaluate binding interactions between receptor and ligand and identify the ligand conformation within the receptor pocket. Currently, various molecular docking programs are extensively applied; therefore, realizing accuracy and performance of the various docking programs could have a significant value. In this comparative study, the performance and accuracy of three widely used non-commercial docking software (AutoDock Vina, 1-Click Docking, and UCSF DOCK) was evaluated through investigations of the predicted binding affinity and binding conformation of the same set of small molecules (HIV-1 protease inhibitors) and a protein target HIV-1 protease enzyme. The tested sets are composed of eight receptor-ligand complexes with high resolution crystal structures downloaded from Protein Data Bank website. Molecular dockings were applied between approved HIV-1 protease inhibitors and the HIV-1 protease using AutoDock Vina, 1-Click Docking, and DOCK6. Then, docking poses of the top-ranked solution was realized using UCSF Chimera. Furthermore, Pearson correlation coefficient (r) and coefficient of determination (r2) between the experimental results and the top scored docking results of each program were calculated using Graphpad prism V9.2. After comparing saquinavir top scored binding poses of each docking program with the crystal structure, various conformational changes were observed. Moreover, according to the relative comparison between the top ranked calculated ?Gbinding values against the experimental results, r2 value of AutoDock Vina, 1-Click Docking, and DOCK6 were 0.65, 0.41, and 0.005, respectively. The outcome of this study shows that the top scored binding free energy could not produce the best pose prediction. In addition, AutoDock Vina results have the highest correlation with the experimental results.

 

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Publication Date
Tue Nov 01 2016
Journal Name
Journal Of Cosmetics, Dermatological Sciences And Applications
Frequency of benign and malignant tumors in localized vitiligo in comparison to generalized and universal vitiligo
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KE Sharquie, AA Noaimi, SJ Murtada…, Journal of Cosmetics, Dermatological Sciences and Applications, 2016 - Cited by 4

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Publication Date
Mon Feb 04 2019
Journal Name
Iraqi Journal Of Physics
Structural and optical properties of CdO and CdO0.99Cu0.01 thin films prepared by pulsed laser deposition technique
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Structural and optical properties of CdO and CdO0.99Cu0.01 thin
films were prepared in this work. Cadmium Oxide (CdO) and
CdO0.99Cu0.01semiconducting films are deposited on glass substrates
by using pulsed laser deposition method (PLD) using SHG with Qswitched
Nd:YAG pulsed laser operation at 1064nm in 6x10-2 mbar
vacuum condition and frequency 6 Hz. CdO and CdO0.99Cu0.01 thin
films annealed at 550 C̊ for 12 min. The crystalline structure was
studied by X-ray diffraction (XRD) method and atomic force
microscope (AFM). It shows that the films are polycrystalline.
Optical properties of thin films were analyzed. The direct band gap
energy of CdO and CdO0.99Cu0.01 thin films were determined from
(αhυ)1/2 v

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Publication Date
Wed Aug 20 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An Evaluation of Serum and Salivary Adipokines (Leptin and Resistin) Levels in Periodontal Health and Disease
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Background: With the start of the current century, increased the interest in the role of the adipose tissue derived substances that named adipokines in the inflammatory diseases of the human being including the inflammatory periodontal disease, but scientific evidences were not clearly demonstrate the association between these adipokines and periodontal pathologies. Materials and Methods: Forty two subjects male only with normal body mass index were selected for the study with an age ranged (30-39 years). Samples were divided into three groups of 14 subjects in each group based on clinical periodontal parameters; clinically healthy gingiva (group I), gingivitis group (group II) and chronic periodontitis patients group (group III), from whom

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Publication Date
Mon Jun 19 2023
Journal Name
Journal Of Engineering
Detection and Removal of Polycyclic Aromatic Hydrocarbon from Selected Areas in Tigris River in Baghdad City
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Aromatic hydrocarbons present in Iraqi national surface water were believed to be raised principally from combustion of various petroleum products, industrial processes and transport output and their precipitation on surface water.
Polycyclic aromatic hydrocarbons (PAHs) were included in the priority pollutant list due to their toxic and carcinogenic nature. The concern about water contamination and the consequent human exposure have encouraged the development of new methods for
PAHs detection and removal.
PAHs, the real contaminants of petroleum matter, were detected in selected sites along Tigris River within Baghdad City in summer and winter time, using Shimadzu high performance liquid chromatography (HPLC) system.
Analysi

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Publication Date
Tue Mar 13 2018
Journal Name
Mustansiria Dental Journal
Dimensional stability of heat-activated acrylic resin at different time intervals by different flask cooling methods
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This study was design to investigate the dimensional stability of heat-activated acrylic resin with different methods of flask cooling (15 minutes rapid cooling, one hour bench cooling, four hours delayed deflasking, and 24 hours delayed deflasking) at different time intervals (immediately, two days, seven days, 30 days) after deflasking. Heat-activated acrylic resin was used to prepare acrylic samples. Then, measurement of the distances where achieved between the centers of selected marks in the acrylic samples. They were measured at different time intervals for different methods of flask cooling. The results showed that the group samples of the four hours and 24 hours of delayed deflasking was insignificantly different from the control an

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Publication Date
Tue Mar 01 2011
Journal Name
Journal Of Kufa For Chemical Science
systhesis,spectral and kinetic of N2O2macrocycle ligand with divalent metal ions ( Co , Ni and Cu ) complexes
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Publication Date
Fri Jan 01 2021
Journal Name
Desalination And Water Treatment
Removal of toxic dye (Rhodamine B) from aqueous solutions by natural smectite (SMC) and SMC-nanoTiO2
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Publication Date
Tue Sep 01 2020
Journal Name
Petroleum
Reversible and irreversible adsorption of bare and hybrid silica nanoparticles onto carbonate surface at reservoir condition
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Realistic implementation of nanofluids in subsurface projects including carbon geosequestration and enhanced oil recovery requires full understanding of nanoparticles (NPs) adsorption behaviour in the porous media. The physicochemical interactions between NPs and between the NP and the porous media grain surface control the adsorption behavior of NPs. This study investigates the reversible and irreversible adsorption of silica NPs onto oil-wet and water-wet carbonate surfaces at reservoir conditions. Each carbonate sample was treated with different concentrations of silica nanofluid to investigate NP adsorption in terms of nanoparticles initial size and hydrophobicity at different temperatures, and pressures. Aggregation behaviour and the

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Publication Date
Fri Dec 01 2023
Journal Name
Russian Journal Of General Chemistry
Preparation, Characterization, and Biological Activity of Mixed Schiff Base Ligand Complexes with Amino Acid L-Proline
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Publication Date
Thu Feb 07 2019
Journal Name
Iraqi Journal Of Laser
Synthesis Characterization and Optical Properties of Nanostructured Zinc Sulfide Thin Films Obtained by Spray Pyrolysis Deposition
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In this work, nanostructure zinc sulfide (ZnS) thin films at temperature of substrate 450 oC and thickness (120) nm have been produced by chemical spray pyrolysis method. The X-Ray Diffraction (XRD) measurements of the film showed that they have a polycrystalline structure and possessed a hexagonal phase with strong crystalline orientation of (103). The grain size was measured using scanning electron microscope (SEM) which was approximately equal to 80 nm. The linear optical measurements showed that ZnS nanostructure has direct energy gap. Nonlinear optical properties experiments were performed using Q-switched 532 nm Nd:YAG laser Z-scan system. The nonlinear refractive index (n2) and nonlinear absorption coefficient (β) estimated for Z

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