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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 Dec 01 2009
Journal Name
Journal Of Economics And Administrative Sciences
Analysis of the theoretical framework of the REA accounting model Used in the design of accounting information systems
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Researchers often equate database accounting models in general and the Resources-Events-Agents (REA) accounting model in particular with events accounting as proposed by Sorter (1969). In fact, REA accounting, database accounting, and events accounting are very different. Because REA accounting has become a popular topic in AIS research, it is important to agree on exactly what is meant by certain ideas, both in concept and in historical origin. This article clarifies the analyzing framework of REA accounting model and highlights the differences between the terms events accounting, database accounting, semantically-modeled accounting, and REA accounting. It als

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Publication Date
Wed Dec 01 2021
Journal Name
Journal Of Economics And Administrative Sciences
A Proposed Mechanism for Financial Reporting on Sustainable Investment and Its Role in Achieving Value Added - Applied in the Iraqi Midland Refineries Company-
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The research aims to develop a proposed mechanism for financial reporting on sustainable investment that takes the specificity of these investments.

To achieve this goal, the researcher used (what if scenario) where the future financial statements were prepared for the year 2026, after completion of the sustainable project and operation, as the project requires four years to be completed.

The researcher relied on the results of the researchers collected from various modern sources relevant to the research topic and published on the internet, and the financial data and information obtained to assess the reality of the company's activity and its environmental, social, and economic i

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Publication Date
Sun May 17 2026
Journal Name
Journal Of Baghdad College Of Dentistry
Evaluation of fracture strength of endodontically treated teeth restored by milled zirconia post and core with different post and core systems (An in vitro comparative study)
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Background: Restoration of root canal treated teeth with a permanent restoration affect in the success of endodontically treated teeth. This in vitro study was performed to evaluate and compare the fracture strength of endodontically treated teeth restored by using custom made zirconium posts and cores, prefabricated carbon fiber, glass fiber and zirconium ceramic posts. Materials and method: Forty intact human mandibular second premolars were collected for this study and were divided into five groups. Each group contains 8 specimens: Group1: Teeth restored with Carbon Fiber Posts; Group2: Teeth restored with Glass Fiber Posts; Group3: Teeth restored with Zirconium Ceramic prefabricated Posts; Group4: Teeth restored with Zirconium Posts

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Publication Date
Thu Sep 02 2021
Journal Name
Solid State Technology
Spectroscopic Investigation of Charge Transfer Complex And Adsorption of Nitrondye with Curcumin(1) Onmodified Attapulgiteclay
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A charge transfer complex formed by interaction between nitron as electron donor with curcumin(1 ) as electron acceptor in ethanol at the temperature of theroom to form a colored complex. The optimum conditions of complex formation were investigated by Univariate method. The linearity range of complex was (3.124– 53.11) μg.mL-1 at 442 nm with molar absorptivity (1858.33) L.mol-1.cm-1, Sandell's sensitivity (0.1681μg.cm-2), and with a correlation coefficient (0.9935). Both modified attapulgite and modified attapulgite – complex have been characterized by using , FTIR, SEM, AFM, and XRD. Theadsorption behaviourof complex onto the modified attapulgite has been researchedthrough the variation of the parameters like the adsorbent weight, p

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Publication Date
Sun Mar 07 2010
Journal Name
Baghdad Science Journal
Darwinian Philosophy as Optimization Method for Design High Reflection Mirror Include New Merit Function
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In this paper we proposes the philosophy of the Darwinian selection as synthesis method called Genetic algorithm ( GA ), and include new merit function with simple form then its uses in other works for designing one of the kinds of multilayer optical filters called high reflection mirror. Here we intend to investigate solutions for many practical problems. This work appears designed high reflection mirror that have good performance with reduction the number of layers, which can enable one to controlling the errors effect of the thickness layers on the final product, where in this work we can yield such a solution in a very shorter time by controlling the length of the chromosome and optimal genetic operators . Res

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Publication Date
Thu Sep 26 2024
Journal Name
Journal Of Optics
Cysteine-cupped CdSe/CdS quantum dots as an opticalbiosensor for early skin cancer detection
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This study represents an optical biosensor for early skin cancer detection using cysteine-cupped CdSe/CdS Quantum Dots (QDs). The study optimizes QD synthesis, surface, optical functionalization, and bioconjugation to enhance specificity and sensitivity for early skin cancer cell detection. The research provides insights into QD interactions with skin cancer biomarkers, demonstrating high-contrast, precise cellular imaging. Cysteine-capped CdSe/CdS absorption spectra reveal characteristic peaks for undamaged DNA, while spectral shifts indicate structural changes in skin-cancer-damaged DNA. Additionally, fluorescence spectra show sharp peaks for undamaged DNA and notable shifts and intensity variations when interacting with skin cancer. This

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Publication Date
Thu Mar 01 2018
Journal Name
Asian Journal Of Multidisciplinary Studies
Entrepreneurial mindset and aspiration as critical success factor for small business performance in Iraq
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The aim of this research is to examine the relationship between entrepreneurial mindset and aspiration and small business performance Baghdad, Iraq. This study proposed a quantitative analysis in which entrepreneurial mindset and aspiration is a critical success factor of small business in Iraq. The method employed in the collection of data was by the means of self-administered questionnaire which was filled and completed by small business owners randomly selected from a sampling frame of registered small businesses. The questionnaire was adapted from the study of Davis, Halls & Mayer (2015) and Abdel-Maksoud, Asada & Nakagawa (2008) which was used to measure entrepreneurial mindset and aspiration using a ten items scale and small business

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Publication Date
Mon Mar 01 2021
Journal Name
Journal Of Physics: Conference Series
Anti-Corrosive Substance as Green Inhibitor for Carbon Steel in Saline and Acidic Media
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Ficus (FIC) leaf extract used as corrosion inhibitor for carbon steel alloy (C.S) in two corrosive environments (saline and acidic) with four concentrations (1, 2, 3 and 4 ppm) at varied temperature range between (298-328 K) using electrochemical polarization measurements. The importance of this work focused on the use the green chemistry that is far from the chemical materials effect. The results of polarization presented the FIC inhibitor consider a mixed type (anodic and cathodic) inhibitor. Tafel curve used to evaluate the corrosion inhibition activity. In a saline medium, the best inhibitor efficiency reaches to (87%) in 2 ppm and IE% reach to (99%) for HCl medium inhibited by 1ppm. Langmuir isotherm obeys the study by thermodynamic pa

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Publication Date
Sat Sep 21 2024
Journal Name
Asian Pacific Journal Of Cancer Prevention
Oncolytic Newcastle Disease Virus and Photodynamic Therapy as Dual Approach for Breast Cancer Treatment
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Objective: We hypothesized that attacking cancer cells by combining various modes of action can hinder them from taking the chance to evolve resistance to treatment. Incorporation of photodynamic therapy (PDT) with oncolytic virotherapy might be a promising dual approach to cancer treatment. Methods: NDV AMHA1 strain as virotherapy in integration with aminolaevulinic acid (ALA) using low power He-Ne laser as PDT in the existing work was examined against breast cancer cells derived from Iraqi cancer patients named (AMJ13). This combination was evaluated using Chou–Talalay analysis. Results: The results showed an increased killing rate when using both 0.01 and 0.1 Multiplicity of infection (MOI) of the virus when combined with a dose of 617

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Publication Date
Wed Nov 01 2017
Journal Name
Biochemical Engineering Journal
Waste date seed oil extract as an alternative feedstock for Poly(3-hydroxybutyrate) synthesis
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