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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 Mar 30 2021
Journal Name
Journal Of Economics And Administrative Sciences
Comparative Study for the Early Detection of the most Important Factors Leading to Preeclampsia
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The aim of this research is to determine the most important and main factors that lead to Preeclampsia. It is also about finding suitable solutions to eradicate these factors and avoid them in order to prevent getting Preeclampsia. To achieve this, a case study sample of (40) patients from Medical City - Oncology Teaching Hospital was used to collect data by a questionnaire which contained (17) reasons to be investigated. The statistical package (SPSS) was used to compare the results of the data analysis through two methods (Radial Bases Function Network) and (Factorial Analysis). Important results were obtained, the two methods determined the same factors that could represent the direct reason which causes Preecla

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Publication Date
Wed Mar 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Effect of Heterogeneity on Capillary Pressure and Relative Permeability Curves in Carbonate Reservoirs. A Case Study for Mishrif Formation in West Qurna/1 Oilfield, Iraq
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The special core analysis tests were accomplished on a set of core plugs for Mishrif Formation (mA, mB1, and mB2cde/mC units) in West Qurna/1 oilfield, southern Iraq. Oil relative permeability (Kro) data and the Corey-type fit of the data as functions of the brine saturation at the core outlet face for individual samples in the water-oil imbibition process to estimate relative permeability measurements by the centrifuge method were utilized. Identical correlations for oil and water relative permeabilities were extracted by steady-state and unsteady-state methods. For the mA samples, the gas-water capillary pressure curves were within a narrow range (almost identical) indicating that mA is a homogeneous unit. Kro curves for thr

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Publication Date
Wed Mar 29 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Effect of Heterogeneity on Capillary Pressure and Relative Permeability Curves in Carbonate Reservoirs. A Case Study for Mishrif Formation in West Qurna/1 Oilfield, Iraq
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The special core analysis tests were accomplished on a set of core plugs for Mishrif Formation (mA, mB1, and mB2cde/mC units) in West Qurna/1 oilfield, southern Iraq. Oil relative permeability (Kro) data and the Corey-type fit of the data as functions of the brine saturation at the core outlet face for individual samples in the water-oil imbibition process to estimate relative permeability measurements by the centrifuge method were utilized. Identical correlations for oil and water relative permeabilities were extracted by steady-state and unsteady-state methods. For the mA samples, the gas-water capillary pressure curves were within a narrow range (almost identical) indicating that mA is a homogeneous unit. Kro curves for three mB2

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Publication Date
Mon Mar 13 2017
Journal Name
Journal Of Baghdad College Of Dentistry
The Effect of Artificial Accelerated Aging on The Color of Ceramic Veneers Cemented With Different Resin Cements (A Comparative In Vitro Study)
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ABSTRACT Background: Color changes that are detectable to human eye can affect the esthetic appearance of ceramic veneers. The purpose of this study was to evaluate and compare the effect of artificial accelerated aging on the color of ceramic veneers cemented with different resin cements. Materials and Methods: Sixty discs were prepared with 0.5 mm thickness, 30 discs made from IPS e.max press (Ivoclar Vivadent) and 30 discs were made from VITA Enamic (VITA Zahnfabrik). The discs were cemented with three resin cements: Variolink Veneer MV 0 shade (Ivoclar Vivadent), Rely X veneer Translucent shade (3M ESPE) and NX3 Nexus Clear shade (Kerr Corporation) with 0.1 mm thickness. The spectrophotometer Easyshade Advance was used to measure the co

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Publication Date
Tue Mar 01 2016
Journal Name
Journal Of Engineering
Critical Success Factors in Construction Projects (Governmental Projects as a Case Study)
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The importance of the construction sector and its Great role in the provision of services and infrastructure, reduce poverty, improve living conditions and improve the economic situation in the country, impose attention to the way in which the projects implemented for its improvement and to get successful projects. The objective of this research was to determine the criteria for success as well as critical success and failure factors that have a significant impact on project success. A selected 75 engineer (department managers, project managers and engineers) are asked to fill  the questionnaire form, Sixty-seven valid questionnaire forms were analyzed statistically to get search results, which were as follows : Twe

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Publication Date
Mon May 12 2025
Journal Name
The International Journal Of The History Of Sport
Exploring Sport’s Role in Mitigating Conflicts Gulf Cup as a Case Study
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Conflict, peace, and sports have a long history as practical realities, and their correlation has become an important subject of study in the last decades of the twentieth century. Sport has infiltrated peace and conflict studies as a tool for resolving conflict and building peace, but opinions have differed between those who say it is a positive tool and others who see it as negative. The Gulf Cup is one of the champions that have never been studied, and in-depth research about it has not been done. This tournament has affected the relations between the states involved. The politics cast its shadow on the Gulf Cup. The paper aims to shed light on how political events in the region have consistently affected the Gulf Cup and how politics in

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Publication Date
Sun Oct 05 2025
Journal Name
Journal Of Baghdad College Of Dentistry
An evaluation of an Iraqi phosphate-bonded investment and a commercial type on the marginal fit of ceramometalcopings using three different investing and burnout techniques
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Background: The accuracy of fitness of any dental casting is imperative for the success of any prosthodontic treatment. From the time that dental casting was first introduced, efforts have been made to produce more accurate and better fitted castings with minimal marginal discrepancy. The aim of this in vitro study was to evaluate the effects of three different investing and burnout techniques on the vertical marginal discrepancies ofceramometalcopings invested with two types of phosphate- bonded investments. Materials and methods: Sixty wax patterns were fabricated on a standardized prepared brass die representing an upper central incisor by the aid of a custom-made split mold. Three different investing and burnout techniques were applied

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Publication Date
Sun Mar 01 2020
Journal Name
Journal Of Engineering
Study the Effect of Particle Sizes and Concentration on the Rheological Properties of Iraqi Bentonite for Using as Drilling Fluids
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The aim of this study is to identify the effect of particle size and to increase the concentration of Iraqi bentonite on rheological properties in order to evaluate its performance and to know if it can be used as drilling fluid without additives or not. In this study, Iraqi bentonite was carried out by mineral composition (XRD), chemical composition (XRF) and Particle size distribution (PSD), and its rheological properties were measured at different particle size and concentration. The results showed that when the particle size of Iraqi bentonite decreased, and the rheological properties were increased with increased concentration of Iraqi bentonite. Also, Iraqi bentonite was unable to use as drilling fluid without certain additives.

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Publication Date
Wed Jan 02 2019
Journal Name
Journal Of Global Pharma Technology
Nanocrystal Technology as a Tool for Improving Dissolution of Poorly Soluble Drugs
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Many approaches have been developed over time to counter the bioavailability limitations of poorly soluble drugs. With advances in nanotechnology in recent decades, this issue has been approached through the formulation of drugs as nanocrystals. Nanocrystals consist of pure drug(s) and a minimum of surface active agent(s) required for stabilization. They are carrier-free submicron colloidal drug delivery systems with a mean particle size typically in the range of 200 - 500 nm. By reducing particle size to nanoscale, the surface area available for dissolution is increased, and thus bioavailability is enhanced. Drug nanocrystals constitute a versatile formulation approach to enhance the pharmacokinetic and pharmacodynamic properties of poorly

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Publication Date
Mon Sep 30 2019
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
A Comparative Study of the Influence of Different Types of Polymers on Viscosity Index and Pour Point of Iraqi Base Oils
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In this study, the effects of blending the un-branched acrylate polymer known as Poly (n-decyl acrylate), and the branched acrylate polymer known as Poly (iso-octyl acrylate), on the viscosity index (VI), and the pour point of the Iraqi base stocks 40, and 60 respectively, were investigated. Toluene was used as a carrier solvent for both polymer types. The improvement level of oils (VI, & pour point) gained by blending the oil with the acrylate derived polymers was compared with the values of (VI, and pour point) gained by blending the oil with a commercial viscosity index, and pour point improver. The commercial lubricant additive was purchased and used by Al-Daura Refineries. It consisted of an un-known olefin copolymer dissolved i

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