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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
Fri Feb 01 2002
Journal Name
Journal Of Engineering /college Of Eng./university Of Baghdad
Study of group action of stone columns using FEM
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Study of group action of stone columns using FEM

Publication Date
Sun Sep 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
Using Six-Sigma to measure the quality performance of the Department of Statistics-University of Baghdad-Case Study
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Abstract

            This research was to provide a definition of quality, dimensions and concepts, whether traditional or modern concept, as well as review the dimensions of quality in higher education and vision and mission with the overall objectives of the Statistics Department.

         After reviewing quality goals and purposes achieved as well as the mechanisms used to achieve them. and use standard Six-Sigma as one of the methodologies used in quality with the historical roots of using this methodology and methods applied and their definitions t

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Publication Date
Sat Dec 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Biosorption of Ciprofloxacin (CIP) using the Waste of Extraction Process of Microalgae: The Equilibrium Isotherm and Kinetic Study
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       Scientists are investigating the efficacy of different biosorbents for promoting economic and environmental viability in purifying contaminants. Among the primary by-products of biodiesel production is waste microalgae biomass, which has the potential to be used as a cheap biosorbent for the treatment of pollution. In the present study, the biomass left over after extracting the chlorella vulgaris was used to test the potential biosorption of CIP from simulated aqueous solutions. Bisorbent's ability was characterized using Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and energy-dispersive X-ray spectroscopy (EDX). Analysis with a Fourier Transform Infrared Spectrometer revealed that C

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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
High Commitment Management and their Impact in Organizational Excellence Afield Research for opinions a sample of managers in the company general Alfurat for chemical industries \Babylon
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In its theoretical framework, this study dealt with the subjects of high commitment management and organizational excellence, as the study came in response to the growing developments and changes in the fields of management. It includes an analysis of correlation and effect between high commitment management, which has been attracting a lot of attention recently due to the intensifying rivalry between organizations because of certain external factors like globalization and world markets liberation, and its effect in achieving organizational excellence.

The practical framework, on the other hand, dealt with the analysis of correlation and effect between the study's variables. The problem

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Publication Date
Sun Jan 01 2023
Journal Name
Organization, Technology And Management In Construction: An International Journal
Using the ordinal priority approach for selecting the contractor in construction projects
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Abstract<p>Effective decision-making process is the basis for successfully solving any engineering problem. Many decisions taken in the construction projects differ in their nature due to the complex nature of the construction projects. One of the most crucial decisions that might result in numerous issues over the course of a construction project is the selection of the contractor. This study aims to use the ordinal priority approach (OPA) for the contractor selection process in the construction industry. The proposed model involves two computer programs; the first of these will be used to evaluate the decision-makers/experts in the construction projects, while the second will be used to formul</p> ... Show More
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Publication Date
Tue Dec 05 2023
Journal Name
Baghdad Science Journal
Red Ginger's Anti-Anxiety Effect on BALB/c Strain Mice (Mus musculus) Pro-Inflammatory and Anti-Inflammatory Measurements as Anxiety Model
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There is a correlation between the occurrence of anxiety and the production of inflammatory mediators, and red ginger rhizome is a well-known herbal product with a high content of phenolic and flavonoid compounds that can be used as anti-inflammatories and antioxidants. The aim of study to evaluate the effect of red ginger as antianxiety in mice (Mus musculus) BALB/c strain by measuring levels of TNF-α, IL-6 and IL-10.  Anxiety model mice were carried out by giving treatment with the Forced Swimming Test (FST) for 7 days then assessed by carrying out the Elevated Plus Maze for Mice (EPM) test for one day. After the treatment, the anxiety mice model was made, followed by administration of red ginger ethanol extract therapy for 14 days.

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Publication Date
Mon Nov 19 2018
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Study of the impact of foreign direct investment in the Iraqi tax system using the factorial analysis: (principal components)
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The tax system, like any other system, as a set of elements and parts that complement each other and are interrelated and interact to achieve specific goals, and is a natural  reflection of the economic, social and political conditions prevailing in society, and therefore the objectives of tax policy formulated in line with the objectives of economic policy in general, which means that any change in economic policy clearly affects fiscal policy measures and fiscal policy in particular.

The problem of searching for the impact of foreign direct investment in the Iraqi tax system was focused on the study  the of foreign direct investment and therole played in developing and improving the economic reality and its implicatio

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Publication Date
Wed Mar 11 2026
Journal Name
Journal Of Baghdad College Of Dentistry
An Evaluation of Ion Released from Two Brands of Brackets in Three Types of Mouthwashes
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Background: Mouthwashes used widely as ancillary to mechanical oral hygiene methods. Little information provided about the effect of mouthwashes on ions released from orthodontic brackets. Therefore, the present study has been established to evaluate the effect of different mouthwashes on the corrosion resistance and the biocompatibility of two brands of brackets. Materials and Methods: Eighty premolar stainless steel brackets were used (40 brackets from each brand). They were subdivided into four subgroups (n=10) according to immersion media (deionized distilled water, Corsodyl, Listerine and Silca herb mouthwashes). Each bracket was stored in a closely packed glass tube filled with 15ml of the immersion media and incubated for 45 days at

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Publication Date
Tue Jan 01 2008
Journal Name
Journal Of Physical Education
Rates of success and failure of some offensive skills composed of three youth basketball skills
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مستخلص البحث كان الهدف من البحث هو معرفة نسب نجاح وفشل بعض المهارات الهجومية المركبة من ثلاث مهارات بكرة السلة للشباب.، إذ لوحظ بأنه لا تكتمل عملية التقدم من خلال إتقان المهارات الأساسية الهجومية المفردة فقط وإنما في القدرة على الدقة والثبات في أداء الربط فيما بينها (التركيب)، وعكس ما تقدم يعد واحد من الأسباب التي تسبب ضعفاً في المستوى ومما يزيد من الأخطاء في الأداء تبعاً لذلك. وفي ضوء ما تقدم تم تصوير ست مباري

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Publication Date
Thu Dec 01 2016
Journal Name
Ama, Agricultural Mechanization In Asia, Africa And Latin America
Effect of three honeycomb interplant distances on growth and flowering of two cultivars of bean
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A factorial experiment (2× 3) in randomized complete block design (RCBD) with three replications was conducted to examine the effect of honeycomb selection method using three interplant distances on the vegetative growth, flowering, and fruit set of two cultivars of bean, Bronco and Strike. Interplant distances used were 75× 65 cm, 90× 78 cm, and 105× 91 cm (row× plant) represent short (high plant density), intermediate (intermediate plant density), and wide (low plant density) distance, respectively. Parameters used for selection were number of days from planting to the initiation of first flower, number of nodes formed prior to the onset of first flower, and number of main branches. Results showed significant superiority of the Strik

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