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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
Sun Jan 01 2023
Journal Name
Results In Chemistry
Synthesis and characterization of (E)-4-(((4-(5-mercapto-1, 3, 4-oxadiazol-2-yl) phenyl) amino) methyl)-2-methoxyphenol as a novel corrosion inhibitor for mild-steel in acidic medium
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Publication Date
Wed Aug 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
A Comparative Study of Some Methods of Estimating Robust Variance Covariance Matrix of the Parameters Estimated by (OLS) in Cross-Sectional Data
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Abstract

The Classical Normal Linear Regression Model Based on Several hypotheses, one of them is Heteroscedasticity as it is known that the wing of least squares method (OLS), under the existence of these two problems make the estimators, lose their desirable properties, in addition the statistical inference becomes unaccepted table. According that we put tow alternative,  the first one is  (Generalized Least Square) Which is denoted by (GLS), and the second alternative is to (Robust covariance matrix estimation) the estimated parameters method(OLS), and that the way (GLS) method neat and certified, if the capabilities (Efficient) and the statistical inference Thread on the basis of an acceptable

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Publication Date
Fri Jan 02 2026
Journal Name
Al–bahith Al–a'alami
THE IMPACT OF ENTERTAINMENT PROGRAMS IN ARAB SATELLITE CHANNELS ON THE SOCIAL BEHAVIOR OF IRAQI YOUTH (Field study)
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Our research is based on the fact that the reflection of entertainment programs in Arab satellite channels on the social behavior of Iraqi youth … a field analysis of the Arab ldol program) and that its importance is the entertainment programs and their reflection on social behavior، which occupies
large areas of time from Satellite channels in the form of various episodes and each episode contains several categories، or in the form of templates and forms of various goals and contents، but the problem of
research boils down to (how far iraqi youth follow the entertainment programs in Arab satellite channels and what are the motives for watching the Program Arab ldol )) by For Iraqi youth and what are the positive and negative

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Publication Date
Tue Jun 30 2020
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Reuse of Brick Waste as a Cheap-Sorbent for the Removal of Nickel Ions from Aqueous Solutions
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   The potential application of granules of brick waste (GBW) as a low-cost sorbent for removal of Ni+2ions from aqueous solutions has been studied. The properties of GBW were determined through several tests such as X-Ray diffraction (XRD), Energy dispersive X-ray (EDX), Scanning electron microscopy (SEM), and BET surface area. In batch tests, the influence of several operating parameters including contact time, initial concentration, agitation speed, and the dose of GBW was investigated. The best values of these parameters that provided maximum removal efficiency of nickel (39.4%) were 1.5 hr, 50 mg/L, 250 rpm, and 1.8 g/100mL, respectively. The adsorption data obtained by batch experiments subjected to the Three i

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Publication Date
Fri Dec 15 2017
Journal Name
Journal Of Baghdad College Of Dentistry
In Vitro Comparative Assessment Of The Effect Of Gutta-Fusion Obturation On The Push Out Bond Strenght Of Three Types Of Sealers
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Background: The bond strength of the root canal sealers to dentin is very important property for maintaining the integrity and the seal of root canal filling. The aim of this study was to evaluate and compare the push-out bond strength of root filled with total fill Bioceramic, AH Plus and Gutta-flow®2 sealers using GuttaFusion®obturation system versus single cone obturation technique. Materials and method: sixty of mandibular premolars teeth with straight roots were used in this study, these roots were instrumented using Reciproc system, instrumentation were done with copious irrigation of 3 mL 5.25% sodium hypochlorite solution (NaOCl) during all the steps of preparation, and smear layer will be removed with 1 ml of 17% EDTA kept in

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Baghdad College Of Dentistry
In Vitro Comparative Assessment of the Effect of Gutta-Fusion Obturation on the Push Out Bond Strength of Three Types of Sealers
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Background: The bond strength of the root canal sealers to dentin is very important property for maintaining the integrity and the seal of root canal filling. The aim of this study was to evaluate and compare the push-out bond strength of root filled with total fill Bioceramic, AH Plus and Gutta-flow®2 sealers using GuttaFusion®obturation system versus single cone obturation technique. Materials and method: sixty of mandibular premolars teeth with straight roots were used in this study, these roots were instrumented using Reciproc system, instrumentation were done with copious irrigation of 3 mL 5.25% sodium hypochlorite solution (NaOCl) during all the steps of preparation, and smear layer will be removed with 1 ml of 17% EDTA kept in

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Publication Date
Sat Jul 20 2024
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Polyacrylonitrile Nanofiber Composites as Efficient Removal of Pollutants for Wastewater: A Review Article
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Polyacrylonitrile nanofiber (PANFS), a well-known polymers, has been extensively employed in the manufacturing of carbon nanofibers (CNFS), which have recently gained substantial attention due to their excellent features, such as spinnability, environmental friendliness, and commercial feasibility. Because of their high carbon yield and versatility in tailoring the final CNFS structure, In addition to the simple formation of ladder structures through nitrile polymerization to yield stable products, CNFS and PAN have been the focus of extensive research as potential production precursors. For instance, the development of biomedical and high-performance composites has now become achievable. PAN homopolymer or PAN-based precursor copolymer can

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Publication Date
Mon Jun 19 2023
Journal Name
Journal Of Polymer Research
Design, and synthesis of a plasticizer- Schiff’s bases complexes as additive for polystyrene
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This work involved the successful synthesis of three new Schiff base complexes, including Ni(II), Mn(II), and Cu(II) complexes. The Schiff base ligand was created by reacting the malonyldihydrazide molecule with naphthaldehyde, and the final step involved reacting the ligand with the corresponding metallic chloride yielding pure target complexes. FTIR, 1 H NMR, 13 C NMR, mass, and UV/Vis spectroscopies were used to comprehensively characterize the produced complexes. These substances have been employed in this study to photo-stabilize polystyrene (PS) and lessen the photo-degradation of its polymeric chains. Several methods, including FTIR, weight loss, viscosity average molecular weight, light and atomic force microscopy, and energy disper

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Publication Date
Mon Sep 04 2017
Journal Name
International Journal Of Environmental Science And Technology
A review of permeable reactive barrier as passive sustainable technology for groundwater remediation
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Publication Date
Tue Apr 25 2023
Journal Name
Journal Of Periodontal Research
Salivary E‐cadherin as a biomarker for diagnosis and predicting grade of periodontitis
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Abstract<sec><title>Objectives

To determine the abilities of salivary E‐cadherin to differentiate between periodontal health and periodontitis and to discriminate grades of periodontitis.

Background

E‐cadherin is the main protein responsible for maintaining the integrity of epithelial‐barrier function. Disintegration of this protein is one of the events associated with the destructive forms of periodontal disease leading to increase concentration of E‐cadherin in the oral biofluids.

Materials and Methods

A total of 63 patients with periodontitis (case) and 35

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