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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 Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Comparing Some Methods of Estimating the Parameters and Survival Function of a Log-logistic Distribution with a Practical Application
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The Log-Logistic distribution is one of the important statistical distributions as it can be applied in many fields and biological experiments and other experiments, and its importance comes from the importance of determining the survival function of those experiments. The research will be summarized in making a comparison between the method of maximum likelihood and the method of least squares and the method of weighted least squares to estimate the parameters and survival function of the log-logistic distribution using the comparison criteria MSE, MAPE, IMSE, and this research was applied to real data for breast cancer patients. The results showed that the method of Maximum likelihood best in the case of estimating the paramete

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Publication Date
Mon Jan 01 2024
Journal Name
5th International Conference On Biomedical And Health Sciences
Exploiting Vpusm 8 Lytic Phage for The Bio- Control of V. Cholerae: A Novel Approach Against Cholera in The Era of Antibiotic Resistance
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Objective: The purpose of this study was to assess the effectiveness of Vibriophage Universiti Sains Malaysia 8 (VPUSM 8), a bacteriophage that destroys bacteria, in managing the proliferation of Vibrio cholerae, specifically the El Tor serotype, as an alternate therapeutic strategy. Methods: The study entailed subjecting water samples from Kelantan, Malaysia, to reproduce the natural circumstances that promote the growth of V. cholerae. Subsequently, the samples were contaminated with the V. cholerae O1 El Tor Inaba strain and treated using VPUSM 8. The study employed a controlled experimental design, wherein the samples were divided into three groups, each experiencing different treatment methods. Quantifying the number of colony-

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Publication Date
Sun Oct 06 2013
Journal Name
Journal Of Educational And Psychological Researches
The Effect of a Behavioral-Cognitive Training Program on Problems Solving among college students in the faculty of education for women : Baghdad University
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The purpose of this study was to investigate the effect of a Cognitive- Behavioral Training Program in reducing Problems Solving among a sample of education university  College Students, the study sample consisted of (50) students were randomly assigned to two groups: experimental, and control; (25) students per group, the results of (ANOVA) revealed that there were significant differences at (p < 0.05) between experimental and control group in Problems Solving level, while there were significant differences between both groups in achievement. The researchers recommended further studies on the other variables which after training students on the method of solving problems and techniques to reduce stress.<

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Publication Date
Sun Aug 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Measuring the impact of corporate governance mechanisms on social responsibility reports for a sample of Iraqi companies listed on the Iraq Stock Exchange
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The study aims to indicate the role of the mechanisms and principles of corporate governance in the activation of social responsibility reports, and increase disclosure, to achieve sustainability, legitimacy, and integrity of the business. Through the presentation of the conceptual framework for corporate governance and social responsibility, identify the key dimensions of social responsibility and the statement of the relationship between the mechanisms of governance and social responsibility reports in accordance with these dimensions. To prove the hypothesis research has selected a sample of listed companies in the Iraqi market for securities,

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Publication Date
Mon Apr 18 2022
The modeling techniques of the second‐order correlation function <i>g</i> <sup>(2)</sup> ( <i>τ</i> ) for a quantum emitter
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Publication Date
Thu Mar 31 2022
Journal Name
Iraqi Geological Journal
Geological Model of the Khabour Reservoir for Studying the Gas Condensate Blockage Effect on Gas Production, Akkas Gas Field, Western Iraq
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The Khabour reservoir, Ordovician, Lower Paleozoic, Akkas gas field which is considered one of the main sandstone reservoirs in the west of Iraq. Researchers face difficulties in recognizing sandstone reservoirs since they are virtually always tight and heterogeneous. This paper is associated with the geological modeling of a gas-bearing reservoir that containing condensate appears while production when bottom hole pressure declines below the dew point. By defining the lithology and evaluating the petrophysical parameters of this complicated reservoir, a geological model for the reservoir is being built by using CMG BUILDER software (GEM tool) to create a static model. The petrophysical properties of a reservoir were computed using

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Publication Date
Thu Jun 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Examining the Asymmetric Impacts of Interest and Exchange Rate on Investment in Egypt for the Period 1976-2020: Applying NARDL Model
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Most of the studies conducted in the past decades focused on the effect of interest rates and exchange rates on domestic investment under the assumption that the independent variables have the same effect on the dependent variable, but there were limited studies that investigated the unequal effects of changes in interest rates and exchange rates, both positive and negative, on domestic investment.  This study used a nonlinear autoregressive distributed lag (NARDL) model to assess the unequal effects of the real interest rate and real exchange rate variables on domestic investment in Egypt for the period 1976 - 2020.  The results revealed that positive and negative shocks for both exchange rates have unequal effects on

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Publication Date
Wed Mar 10 2021
Journal Name
Baghdad Science Journal
Synthesis of Bimetallic Au–Pt / TiO2 Catalysts as an Efficient Catalyst for the Photodegradation of Crystal Violet Dye
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     Bimetallic Au –Pt catalysts supporting TiO2 were synthesised using two methods; sol immobilization and impregnation methods. The prepared catalyst underwent a thermal treatment process at 400 C, while the reduction reaction under the same condition was done and the obtained catalysts were identified with transmission electron microscopy (TEM) and energy-dispersive spectroscopy (EDS). It has been found that the prepared catalysts have a dimension around 2.5 nm and the particles have uniform orders leading to high dispersion of platinum molecules .The prepared catalysts have been examined as efficient photocatalysts to degrade the Crystal violet dye under UV-light. The optimum values of Bimetallic Au –

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Publication Date
Mon Nov 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of the cleaning efficiency of the isthmus using different rotary instrumentation techniques (In vitro study)
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Background: The aims of the study were to evaluate the unclean/clean root canal surface areas with a histopathological cross section view of the root canal and the isthmus and to evaluate the efficiency of instrumentation to the isthmus using different rotary instrumentation techniques. Materials and Methods:The mesial roots of thirty human mandibular molars were divided into six groups, each group was composed of five roots (10 root canals)which prepared and irrigated as: Group one A: Protaper system to size F2 and hypodermic syringe, Group one B: Protaper system to size F2 and endoactivator system, Group two A:Wave One small then primary file and hypodermic syringe, Group two B:Wave One small then primary file and endoactivator system, Gr

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Publication Date
Sat Dec 02 2023
Journal Name
Bulletin Of The Iraq Natural History Museum
MORPHOLOGICAL AND MOLECULAR STUDIES OF KAIS KINGFISH CYPRINION KAIS HECKEL, 1843 (PISCIES, CYPRINIFORMES, CYPRINIDAE) FROM THE MIDDLE OF IRAQ
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Cyprinidae species are the most abundant and widely distributed fish species in the inland waters of Iraq. Cyprinids are complex species, and it is difficult to identify them on the basis of morphology. Thus, the morphological characteristics must be achieved and confirmed by molecular analysis. Twenty specimens of Cyprinion kais Heckel, 1843 (Piscies, Cypriniformes, Cyprinidae) were collected from two localities at Tigris River in the middle of Iraq: five specimens from Al-Tharthar Lake, Saladin Province, and 15 specimens from Al- Zubaydiyah sub-district, Wasit Province

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