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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
Sun May 02 2021
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Application of banking institutions' governance variables and their impact on financial performance as measured by (ROA & ROE): an applied study on a sample of local Islamic banks listed on the Iraq Stock Exchange
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The research seeks to achieve its goal of demonstrating the impact of applying banking governance variables on the financial performance of Islamic banks, and the independent research variables are represented by (X) by (the number of independent members in the board (X1), the number of directors in the board (X2), the number of committees emanating from the board ( X3), the percentage of shares owned by major shareholders in the board (X4), the number of members of the Sharia supervisory board (X5)), and the dependent variable (Y) is represented by (rate of return on assets (Y1), rate of return on equity (Y2)).

The research sample included (4) Islamic banks, namely (Iraqi Islamic Bank, National Islamic Bank, Jihan Islamic Bank,

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Publication Date
Mon Jun 01 2020
Journal Name
Journal Of Engineering Science And Technology
The feasibility of using styrene-butadiene-styrene (SBS) as modifier in Iraqi bituminous binder
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The increase in the number of trucks and other heavy vehicles in Iraqi highways lead to cracking and deteriorations in the flexible highway. The use of polymermodified asphalt may solve this problem to match the required performance standards. This study investigates the effects of styrene-butadiene-styrene (SBS) polymer on the performance behaviour of Iraqi bitumen binder. The characteristics of bitumen binder were analysed to observe the compatibility of bitumen with SBS polymer. The bitumen binder was mixed with three different contents of SBS (4%, 4.5%, and 5%) by weight of asphalt cement. Viscosity tests were conducted on the SBS polymer-modified asphalt at 135 oC and 165 oC in addition to conventional binder tests. The prepar

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Publication Date
Sat Aug 23 2025
Journal Name
Journal Of Economics And Administrative Sciences
The role of public relations in enhancing the quality of governmental service-a Field study in the Iraqi Airlines
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Publication Date
Tue Nov 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
The role of public relations in enhancing the quality of governmental service-a Field study in the Iraqi Airlines
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Abstract
        The research has discussed the public relations as dependent variable of its branch dimensions( confidence , commitment, control and satisfaction ) and the governmental service quality as independent variable of its branch dimensions (response, dependency, emphasis, tangibility and sympathy), and the research problem has represented by weakness of service quality presented to the customers dealing with company, which is observed via  field co-existence of the researcher, where he observe that the quality presented in the company services, are inappropriate with the customers expectations level, also there is weakness of attention and recognition by the

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Publication Date
Thu Jan 13 2022
Journal Name
Journal Of Water And Land Development
A study of the climate and human impact on the future survival of the Al-Sannya marsh in Iraq
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Polish Academy of Sciences

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Publication Date
Sat Aug 23 2025
Journal Name
Journal Of Baghdad College Of Dentistry
The effects of various beverages on the shear bond strength of light-cured orthodontic composite (An in vitro comparative study)
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Background: This study was conducted to assess the effects of various beverages on the shear bond strength of light-cured orthodontic composite used to bond stainless steel orthodontic brackets on human teeth and to determine the site of bonding failure of this material. Materials and Methods: Fifty extracted human premolars were selected and randomly divided into five equal groups each with 10 teeth according to the beverage type (Control, One Tiger, Milk, Green tea and Coffee). After bonding, the teeth were immersed in specific beverages for 5 minutes twice daily with equal intervening intervals then washed and stored in distilled water at 37º C for the reminder of the day. The process was carried out for 30 days. The samples were then

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Publication Date
Thu Feb 29 2024
Journal Name
International Journal Of Safety And Security Engineering
Urban Safety is a Tool for Containing Slums to Reach a Sustainable Urban Structure
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Many cities suffer from the large spread of slums, especially the cities of the Middle East. The purpose of the paper is to study the reality of informal housing in Al-Barrakia and the most important problems that it suffers from. The paper also seeks to study the presence or absence of a correlation between urban safety indicators and urban containment indicators as one of the methods of developing and planning cities. This can be achieved through sustainable urban management. The slums are a source of many urban problems that threaten the security and safety of the residents and represent a focus for the concentration of crimes and drugs. The paper seeks to answer the following question: How can urban safety be improved through urban cont

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Publication Date
Wed Aug 30 2023
Journal Name
Al-kindy College Medical Journal
‘Peacock tail’ Clipping Technique for a Giant Middle Cerebral Artery Aneurysm: A Technical Note
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Background: Giant middle cerebral artery (MCA) aneurysms are surgically challenging lesions. Because of the complexity and variability of these aneurysms, a customized surgical technique is often needed for each case. In this article, we present a modified clip reconstruction technique of a ruptured complex giant partially thrombosed middle cerebral artery aneurysm.

Case description: The aneurysm was exposed using the pterional approach. Following proximal control, the aneurysm sac was decompressed. Then, we applied permanent clips to reconstruct the aneurysm neck. The configuration of the aneurysm mandated a tailored clipping pattern to account for resi

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Publication Date
Wed Jun 09 2021
Journal Name
International Journal Of Environmental Science And Technology
Water quality index toward a reliable assessment for water supply uses: a novel approach
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Publication Date
Sun Sep 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Measurement of economic returns and environmental and social for green sector trade A prospective study in institutions of Basra to focus on the electricity sector
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        Environmental risk growing Become challenge "and a matter of controversy and concern to many of those concerned with environment, social, economic, and the same happens with the administrative rather than in isolation for this movement, as the issues of climate change Disturbed and troubled him, especially after what caused the risk of destruction, and irresponsibility , chaos, and the futility of resources, crops, fields,  nature and homes and reactors, and after what happened in Japan from the scourge of "Hurricane tsunami " and earthquakes successive accompanied him and what became of him by surprise catastrophic affected the economy and the univ

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