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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
Thu Mar 01 2018
Journal Name
Case Studies In Thermal Engineering
The temperatures distributions of a single-disc clutches using heat partitioning and total heat generated approaches
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Publication Date
Mon Mar 11 2019
Journal Name
Al-khwarizmi Engineering Journal
An Investigation Study of Tool Geometry in Single Point Incremental Forming (SPIF) and their effect on Residual Stresses Using ANOVA Model
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Incremental forming is a flexible sheet metal forming process which is performed by utilizing simple tools to locally deform a sheet of metal along a predefined tool path without using of dies. This work presents the single point incremental forming process for producing pyramid geometry and studies the effect of tool geometry, tool diameter, and spindle speed on the residual stresses. The residual stresses were measured by ORIONRKS 6000 test measuring instrument. This instrument was used with four angles of (0º,15º,30º, and 45º) and the average value of residual stresses was determined, the value of the residual stress in the original blanks was (10.626 MPa). The X-ray diffraction technology was used to measure the residual stresses

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Publication Date
Tue Sep 08 2020
Journal Name
Baghdad Science Journal
Convergence Analysis for the Homotopy Perturbation Method for a Linear System of Mixed Volterra-Fredholm Integral Equations
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           In this paper, the homotopy perturbation method (HPM) is presented for treating a linear system of second-kind mixed Volterra-Fredholm integral equations. The method is based on constructing the series whose summation is the solution of the considered system. Convergence of constructed series is discussed and its proof is given; also, the error estimation is obtained. Algorithm is suggested and applied on several examples and the results are computed by using MATLAB (R2015a). To show the accuracy of the results and the effectiveness of the method, the approximate solutions of some examples are compared with the exact solution by computing the absolute errors.

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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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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
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 Apr 04 2022
Journal Name
Journal Of Educational And Psychological Researches
The Role of a University Professor in the Development of Democracy with the Contents of a University Student in the Light of a Democratic Society
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The current research aims to answer the following questions: what is the substance of democracy? What is the content of a democratic society? What is the role of university professor in the democratic development of the student university in light of the new Iraqi society? In order to achieve the goals of the research, the researcher developed an a questionnaire based on literature, Iraq's draft constitution in 2005, and his experience of the field of teaching human rights and public freedoms and the teaching of democracy. It was applied to a sample of faculty members in Department of Education and Psychology / College of Education / University Baghdad for the year 20014 were obtained their answers were then processed statistically. Henc

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Publication Date
Wed Jan 01 2025
Journal Name
Lecture Notes In Networks And Systems
Using Artificial Intelligence to Enhance Digital Media Literacy Competencies and its Role in Shaping Media Students’ Awareness of Cybersecurity: A Survey Study
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Publication Date
Mon Dec 21 2020
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
COMPARATIVE STUDY OF SEVERAL MORPHOLOGICAL AND REPRODUCTIONAL ASPECTS FOR SOME SPECIES OF THE BELLEVALIA LAPEYROUSE, 1808 AND ORNITHOGALUM LINNAEUS, 1753 (ASPARAGALES, ASPARAGACEAE) IN CENTRAL AND NORTH OF IRAQ
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This study aims to study some morphological and reproductional characteristics in eleven species of two genera belonging to the family of Asparagaceae, which are Bellevalia Lapeyrouse, 1808 and Ornithogalum Linnaeus, 1753 and the species are: Bellevalia chrisii Yildirim and Sahin, 2014; Bellevalia flexuosa Boissier, 1854; Bellevalia kurdistanica Feinbrun, 1940; Bellevalia longipes Post, 1895; Bellevalia macrobotrys Boissier, 1853; Bellevalia paradoxa Boissier, 1882; Bellevalia parva Wendelbo, 1973; Bellevalia saviczii Woronow, 1927; Ornithogalum brachystachys C. Koch, 1849; Ornithogalum neurostegium Boissier, 1882 and Ornithogalum pyrenaicum Linnaeus, 1753. These species were identified and compared with each other; the results showed th

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Publication Date
Mon Dec 09 2019
Journal Name
Periodicals Of Engineering And Natural Sciences
The philosophy of the workplace spirituality in the third millennium organizations: A field study at the ministry of health center
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Purpose: The research aims to build an integrated knowledge framework for the basic research topic. The spirituality of the workplace is through access to the most important scientific proposals on these topics. In management thought framing, the knowledge within them in a serious attempt is to provide the appropriate answers about the intellectual dilemma of research by diagnosing the nature of the relationship with the influential elements and its historical development . Methodology: The study is relied on the analytical survey method. The research sample targeted (88) managers in the center of the Iraqi Ministry of Health exclusively from the researched senior leaders (general manager, assistant general manager, and head of department),

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