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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 Jun 06 2020
Journal Name
Journal Of The College Of Education For Women
The Role of School Administration on Academic Achievement in Khartoum International Institute for Arabic language: A Practical Study
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School administration has an effective role in stimulating academic achievement, as it is the ideal regulation and activation of material and human power to achieve the goals of the educational process. This role has axes in the form of interests, aids, and specific procedures exercised by the school administration in improving the educational process, and assisting researchers in achieving the highest levels of academic achievement. This activation is achieved through stages of planning, organizing, coordinating, and evaluating.

To achieve the aims of this research, the researcher pursued the descriptive analytical approach, which is considered one of the most appropriate approaches to the nature of this type of research. The qu

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Publication Date
Thu Jul 01 2021
Journal Name
Iraqi Journal Of Science
The Influence of NMI against Modularity in Community Detection Problem: A Case Study for Unsigned and Signed Networks
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Community detection is useful for better understanding the structure of complex networks. It aids in the extraction of the required information from such networks and has a vital role in different fields that range from healthcare to regional geography, economics, human interactions, and mobility. The method for detecting the structure of communities involves the partitioning of complex networks into groups of nodes, with extensive connections within community and sparse connections with other communities. In the literature, two main measures, namely the Modularity (Q) and Normalized Mutual Information (NMI) have been used for evaluating the validation and quality of the detected community structures. Although many optimization algo

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Publication Date
Wed Mar 29 2023
Journal Name
Journal Of The College Of Education For Women
A Cognitive Linguistic Study of the Present Simple: An Experimental Study in the University of Baghdad
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Some research reports that cognitive grammar (CG) theory has good contributions to teaching English as a foreign language. In this research, the researchers seek to apply this theory and its principles when teaching the simple present tense to Iraqi students who face difficulties in differentiating between the multiple usages of this tense. To achieve this objective, the researchers have conducted an experimental study on a group of 60 Iraqi students in the University of Baghdad, College of Education for Women. Langacker’s (2003) theory has been adopted in the analysis of the cognitive relations to understand the common and different connections of these usages of the simple present. The study has concluded that the cognitive grammar t

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Publication Date
Sat Oct 01 2022
Journal Name
Case Studies In Thermal Engineering
Comparative assessment of the performance and combustion attributes of a free piston linear generator fuelled with CNG and CNG-CO2
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Publication Date
Thu Dec 15 2022
Journal Name
Bionatura
NDRG1 is being investigated as a possible bladder cancer biomarker in the Iraqi population.
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With 549,393 new cases recorded in 2018, bladder cancer is one of the most common malignancies worldwide. Urinary bladder cancer is the cause of about 3 percent of all new cancer diagnoses and 2.1 percent of all cancer deaths. This study aims to evaluate the efficiency of the N-myc downstream-regulated gene 1(NDRG1) as a biomarker for bladder cancer patients in the Iraqi population. One hundred individuals in the case-control study were enrolled and divided into two groups. The first group included 50 patients diagnosed with a bladder mass and investigated by undergoing cystoscopy examination for transurethral resection of bladder tumor (TURB). The second group included 50 healthy individuals who had normal bladder tissue. The resul

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Publication Date
Wed Jun 30 2021
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
BANKING COMPLIANCE FUNCTION(COMPARATIVE STUDY BETWEEN COMMERCIAL & ISLAMIC BANKS): BANKING COMPLIANCE FUNCTION(COMPARATIVE STUDY BETWEEN COMMERCIAL & ISLAMIC BANKS)
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Never the less, banking compliance function became one of the most important functions in banking sector according to its characteristics that considered as an interior control tools to control (executive management, departments, subsidiaries…etc) in any bank; and their compliance towards applying rules, recommendations and legislations. In addition to, estimating the risks and limited them; and controlling the anti-money laundering. Thus, these functions that covered the main concept of (Banking Compliance) would avoid the bank to be under the control of any sanctions.

 

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Publication Date
Sun Dec 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
The Determinants of Total Factor Productivity Growth: an Analytical Study of a Cross Section of Countries for the Period (2003-2016)
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            This study tests the effect of a large number of independent variables that control the growth of the total productivity, which amounted to 112 variables, gathered from what is mentioned in the specialized theoretical and applied literature. The data for these variables were taken from global reports of sound international organizations and reliable databases covering the period 1991-2016. The data of the dependent variable, the growth of the total factor productivity, were taken from the database of the world development indicators. The study covered 61 countries for which data were available. The study included three regression models to explain

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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
A New Green Approach of CFIA Technique for Direct Assay with a High Throughput of Sulfamethoxazole Drugs Using Condensation Reaction with NQS Agent
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A new design of manifold flow injection (FI) coupling with a merging zone technique was studied for sulfamethoxazole determination spectrophotometrically. The semiautomated FI method has many advantages such as being fast, simple, highly accurate, economical with high throughput . The suggested method based on the production of the orange- colored compound of SMZ with (NQS)1,2-Naphthoquinone-4-Sulphonic acid Sodium salt in alkaline media NaOH at λmax 496nm.The linearity range of sulfamethoxazole was  3-100  μg. mL-1, with (LOD) was 0.593 μg. mL-1 and the RSD% is about 1.25 and the recovery is 100.73%. All various physical and chemical parameters that have an effect on the stability and development of

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Publication Date
Sat Apr 13 2019
Journal Name
Journal Of The College Of Languages (jcl)
A Study of Collocation in English
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We used to think of grammar as the bones of the language and vocabulary as the flesh to be added given that language consisted largely of life generated chunks of lexis. This “skeleton image” has been proverbially used to refer to that central feature of lexis named collocation- an idea that for the first 15 years of language study and analysis gave a moment‟s thought to English classroom material and methodology.
The work of John Sinclair, Dave Willis, Ron Carter, Michael McCarthy, Michael Lewis, and many others have all contributed to the way teachers today approach the area of lexis and what it means in the teaching/learning process of the language. This also seems to have incorporated lexical ideas into the teaching mechanis

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Publication Date
Fri May 16 2014
Journal Name
International Journal Of Computer Applications
A Comprehensive Study of Smart Grids
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In this paper, various aspects of smart grids are described. These aspects include the components of smart grids, the detailed functions of the smart energy meters within the smart grids and their effects on increasing the awareness, the advantages and disadvantages of smart grids, and the requirements of utilizing smart grids. To put some light on the difference between smart grids and traditional utility grids, some aspects of the traditional utility grids are covered in this paper as well.

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