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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
Wed Nov 26 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of marginal gap at the composite/enamel interface in Class II composite resin restoration by SEM after thermal and mechanical load cycling (An in vitro comparative study)
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Background: This study compared in vitro the marginal adaptation of three different, low shrink, direct posterior composites Filtekâ„¢ P60 (packable composite), Filtekâ„¢ P90 (Silorane-based composite) and Sonic fillâ„¢ (nanohybrid composite) at three different composite/enamel interface regions (occlusal, proximal and gingival regions) of a standardized Class II MO cavity after thermal changes and mechanical load cycling by scanning electron microscopy. Materials and methods:Thirty six sound human maxillary first premolars of approximately comparable sizes were divided into three main groups of (12 teeth) in each according to the type of restorative material that was used: group (A) the teeth were restored with Filtekâ„¢ P6

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Publication Date
Thu Jan 01 2015
Journal Name
International Journal Of Optics And Applications
Modeling and Analysis of a Miniaturized Ring Modulator Using Silicon-Polymer-Metal Hybrid Plasmonic Phase Shifter. Part II: Performance Predictions
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The ring modulator described in part I of this paper is designed here for two operating wavelengths 1550nm and 1310nm. For each wavelength, three structures are designed corresponding to three values of polymer slot widths (40, 50 and 60nm). The performance of these modulators are simulated using COMSOL software (version 4.3b) and the results are discussed and compared with theoretical predictions. The performance of intensity modulation/direct detection short range and long rang optical communication systems incorporating the designed modulators is simulated for 40 and 100Gb/s data rates using Optisystem software (version 12). The results reveal that an average energy per bit as low as 0.05fJ can be obtained when the 1550nm modulator is d

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Publication Date
Thu Jan 01 2015
Journal Name
International Journal Of Optics And Applications
Modeling and Analysis of a Miniaturized Ring Modulator Using Silicon-Polymer-Metal Hybrid Plasmonic Phase Shifter. Part I: Theoretical Framework
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This paper presents comprehensive analysis and investigation for 1550nm and 1310nm ring optical modulators employing an electro-optic polymer infiltrated silicon-plasmonic hybrid phase shifter. The paper falls into two parts which introduce a theoretical modeling framework and performance assessment of these advanced modulators, respectively. In this part, analytical expressions are derived to characterize the coupling effect in the hybrid phase shifter, transmission function of the modulator, and modulator performance parameters. The results can be used as a guideline to design compact and wideband optical modulators using plasmonic technology

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Publication Date
Tue Jun 07 2022
Journal Name
Journal Of Nuclear Engineering And Radiation Science
Radon and Exhalation Rate Measurement of Soil Samples in Al-Amiriya Area in Baghdad Governorate Using a Nuclear Track Detector
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Abstract<p>Radon is the most dangerous natural radioactive component affecting the human population, since it is a radioactive gas that results from the decomposition process of uranium deposits in soil, rocks, and water, and it is damaging both humans and the ecosystem. The radon concentrations and exhalation rate in soil samples from various locations were determined using a passive approach with a CR-39 (CR-39 is Columbia Resin #39; it is allyl diglycol carbonate C12H18O7) detector in Amiriya region in Baghdad Governorate. The average values of radon concentrations are ranged from 47.3 to 54.2 Bq·m−3. From the obtained results, we can conclude that the values of all studied locations are</p> ... Show More
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Publication Date
Sun Jan 01 2023
Journal Name
Desalination And Water Treatment
Optimization of chemical oxygen demand removal from petroleum refinery wastewater by electrocoagulation using tubular electrochemical reactor with a novel design
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Publication Date
Wed Sep 14 2016
Journal Name
Journal Of Baghdad College Of Dentistry
Expression of Syndecan 1 on Periodontium treated with Topical Application of Aloe-Vera
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Background: Periodontium mainly exposed to injury by trauma or pathologic diseases, Aloe vera is a plant has many basic ingredients in its extracted gel that acts as wound healing accelerator in addition to that it's safe, and economical and without recordable of side effect. This study aimed is to evaluate the effect of topical application of Aloe vera on expression of syndecan -1 by periodontium tissue. Materials and methods: Thirty six male Albino rats were subjected for periodontium defect by electric scaler on the distal sides of both lower anterior teeth. The animals divided into two groups; control group (without treatment) and the experimental group treated with 1µLAloe vera gel/normal saline. Periodontal healing was examined at

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Publication Date
Mon May 01 2023
Journal Name
Journal Of Engineering
Experimental Investigation of Heat Transfer Enhancement in a Double Pipe Heat Exchanger Using Compound Technique of Transverse Vibration and Inclination Angle
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Numerous tests are recently conducted to assess vibration's role in accelerating the heat transfer rate in various heat exchangers. In this work, the enhancement of heat transfer by the effect of transfer vibration and inclination angles on the surface of a double pipe heat exchanger experimentally has been investigated. A data acquisition system is applied to record the data of temperatures, flow rates, and frequencies over the tests. A compound technique was adopted, including the application of a set of inclination angles of (0°, 10°, 20°, and 30°) under the effect of frequency of vibration ranging from sub-resonance to over-resonance frequencies. The results showed that the overall heat transfer coefficient enhan

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Publication Date
Tue Nov 24 2020
Journal Name
Experimental Heat Transfer
Thermal performance of a flat-plate solar collector using aqueous colloidal dispersions of multi-walled carbon nanotubes with different outside diameters
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The thermal performance of a flat-plate solar collector (FPSC) using novel heat transfer fluids of aqueous colloidal dispersions of covalently functionalized multi-walled carbon nanotubes with β-Alanine (Ala-MWCNTs) has been studied. Multi-walled carbon nanotubes (MWCNTs) with outside diameters of (< 8 nm) and (20–30 nm) having specific surface areas (SSAs) of (500 m2/g) and (110 m2/g), respectively, were utilized. For each Ala-MWCNTs, waterbased nanofluids were synthesized using weight concentrations of 0.025%, 0.05%, 0.075%, and 0.1%. A MATLAB code was built and a test rig was designed and developed. Heat flux intensities of 600, 800, and 1000 W/m2; mass flow rates of 0.6, 1.0, and 1.4 kg/min; and inlet fluid temperatures of 30, 40, an

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Publication Date
Tue Dec 01 2015
Journal Name
Journal Of Economics And Administrative Sciences
The impact of the integrative role of the Business Intelligence system and Knowledge Conversion Processes in Building a learning organization A field research in Korek telecom company in Baghdad city
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Purpose:  The research aims to explore the impact Business Intelligence System (BIS) and Knowledge Conversion Processes (KCP) in the Building Learning Organization (LO) in KOREK Telecom Company in Baghdad city.

Design/methodology/approach: in order to achieve the objectives of the research has been the development of a questionnaire prepared for this purpose and then has tested the search in the telecommunications sector, representatives of one of the telecommunications companies in Baghdad city, has therefore chosen KOREK Telecom company as a sample for research, and the choice was based on the best standard international companies to serve mobile communications in terms o

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Publication Date
Tue Jan 01 2019
Journal Name
Indian Journal Of Public Health Research &amp; Development
A 4-Day Plaque-Regrowth Anti-Plaque Effect of a Combination of Green Tea and Salvadora Persica L.: A Randomized Controlled Crossover Clinical Trial
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