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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
Sat Nov 22 2025
Journal Name
Al–bahith Al–a'alami
The Impact of Financial Financing on the Future of the Iraqi Print Press, A Survey Study by the Contactor
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The objectives of this study revolve around identifying the extent of funding impact on the future of the printed Iraqi press, and whether it threatens their chances of survival, stating the extent of technological development on the income of the printed newspaper, and identifying the causes of the financial crisis on the newspaper.
This research is classified as descriptive research, and the researcher used the survey method, and adopted the questionnaire of the views of the contactors, in five Iraqi newspapers (morning - extent - time - the way of the people - the call).
The research community included (68) respondents, whereby the comprehensive inventory method was used to define the research community, and the researcher used

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Publication Date
Tue Sep 09 2014
Journal Name
Iosr Journal Of Mathematics (iosr-jm)
An Efficient Shrinkage Estimator for the Parameters of Simple Linear Regression Model
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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
Studying the Behavior of Asphalt Stabilized Gepseous Soil for Earth Embankment Model
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The study presents the test results of stabilizing gypseous soil embankment obtained from
Al- Faluja university Campus at Al-Ramady province. The laboratory investigation was divided
into three phases, The physical and chemical properties, the optimum liquid asphalt (emulsion)
requirements (which are manufactured in Iraq) were determined by using one dimensional
unconfined compression strength test.in the first phase , The optimum fluid content was 11%
(6% of emulsion with 5% water content).. At phase two, the effect of Aeration technique was
investigated using both direct shear and permeability test. At phase three for the case of static
load , the pure soil embankment model under dry test condition was investigated

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Publication Date
Sun Jan 01 2023
Journal Name
Chemical Engineering And Processing - Process Intensification
Optimization of a combined electrocoagulation-electro-oxidation process for the treatment of Al-Basra Majnoon Oil field wastewater: Adopting a new strategy
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The performance of a synergistic combination of electrocoagulation (EC) and electro-oxidation (EO) for oilfield wastewater treatment has been studied. The effect of operative variables such as current density, pH, and electrolyte concentration on the reduction of chemical oxygen demand (COD) was studied and optimized based on Response Surface Methodology (RSM). The results showed that the current density had the highest impact on the COD removal with a contribution of 64.07% while pH, NaCl addition and other interactions affects account for only 34.67%. The optimized operating parameters were a current density of 26.77 mA/cm2 and a pH of 7.6 with no addition of NaCl which results in a COD removal efficiency of 93.43% and a specific energy c

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Publication Date
Sat Jul 01 2017
Journal Name
Journal Of Biological Chemistry
Functional and phylogenetic evidence of a bacterial origin for the first enzyme in sphingolipid biosynthesis in a phylum of eukaryotic protozoan parasites
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Publication Date
Sun Jan 01 2023
Journal Name
Chemical Engineering And Processing - Process Intensification
Optimization of a combined electrocoagulation-electro-oxidation process for the treatment of Al-Basra Majnoon Oil field wastewater: Adopting a new strategy
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Publication Date
Sun Dec 31 2023
Journal Name
Nativa,
Benthic invertebrate at three sites on the Tigris River, Iraq
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The study was conducted from November 2021 to May 2022 at the three study sites within the Baghdad governorate. The study aims to identify the impact of human activities on the Tigris River, so an area free of human activities was chosen and represented the first site. A total of 48 types were diagnosed, 6204 ind/m3 spread over three sites. The following environmental indicators were evaluated: Constancy Index (S), Relative abundance index (Ra), Richness Index (between 17.995 and 23.251), Shannon Weiner Index (0.48-1.25 bit/ind.), Uniformity Index (0.124 -0.323). The study showed that the highest percentage recorded was for the phylum Annileda 34%; and the stability index shows that taxes (Stylaria sp., Aoelosoma sp., Branchinra sowerby, Ch

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Publication Date
Fri Mar 01 2024
Journal Name
Baghdad Science Journal
Comparative Study of Genomic DNA Extraction Protocols from Whole Blood for P53 Gene Polymorphism in Persons with and without Prostate Cancer
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In latest decades, genetic methods have developed into a potent tool in a number of life-attaching applications. In research looking at demographic genetic diversity, QTL detection, marker-assisted selection, and food traceability, DNA-based technologies like PCR are being employed more and more. These approaches call for extraction procedures that provide efficient nucleic acid extraction and the elimination of PCR inhibitors. The first and most important stage in molecular biology is the extraction of DNA from cells. For a molecular scientist, the high quality and integrity of the isolated DNA as well as the extraction method's ease of use and affordability are crucial factors. The present study was designed to establish a simple, fast

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Publication Date
Mon Jul 01 2019
Journal Name
Iop Conference Series: Materials Science And Engineering
Study the Effect of Cyperus Rotundus Extracted as Mouthwash on the Corrosion of Dental Amalgam
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Many extracted material were used as mouthwash to settle different kinds of oral fungi and bacteria. In this study an extractive of Cyperus rotundus plant E.C.R. which is very active as a mouthwash, was used in concentration range (10-25) ppm in artificial saliva at pH=6.4 and temperature range (288-318) K, to study it’s inhibitory effect on the corrosion of dental amalgam. Potentiostatic and cyclic polarization were used to follow this study. The presence of E.C.R. lead to shift the corrosion potential to the active direction and decreased the corrosion rate to about 98.87%, the inhibition action of E.C.R. resulting from the adsorption of C.R.E. layer between amalgam and saliva as FTIR spectrums shows, where the variety of FTIR adsorptio

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Publication Date
Mon Aug 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
The Role of Moral Intelligence of Internal Auditors in Support of the Performance of Internal Audit Process - Study for Opinions of a Sample of Internal Auditors in Iraq
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Abstract

      The  aim of  the research to define the concept of moral intelligence and its dimensions and its relationship to some personal characteristics with the internal auditors and identify the importance of the employment of moral intelligence dimensions of (empathy, conscience, self- control, respect, kindness, tolerance, fairness) in the internal audit and the extent of support for the performance of the internal audit process in light of these dimensions. And that by answering the following question : Is there a role for moral intelligence  of  internal auditors in support the performance of internal audit process ? How are employ these dimensions i

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