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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 Mar 01 2026
Journal Name
Journal Of Baghdad College Of Dentistry
The effect of orthodontic relapse on the proliferation of fibroblast and epithelial rests of Malassez in periodontal ligament of rat molars (A histopathological study)
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Background: Relapse of previously moved teeth, is major clinical problem in orthodontics with respect to the goals of successful treatment. This study investigated the effect of orthodontic relapse on the proliferation of fibroblast and epithelial rests of Malassez cells in periodontal ligament of rat molars. Materials and Methods: Sixteen ten-week- old male Wister rats were randomly divided into four groups composed of four animals each: Group I received no orthodontic force (control). In both Group II and Group III, uniform standardized expansive springs were used for moving the maxillary first molars buccally for periods of one and three weeks respectively. The spring initially generated an average expansive force of 20 g on each side.

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Publication Date
Thu Dec 14 2023
Journal Name
Optical And Quantum Electronics
Enhancing response characteristics of palladium-doped vanadium pentoxide on a porous silicon substrate as gas sensor synthesized by pulsed laser deposition
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Publication Date
Sun Mar 02 2014
Journal Name
Baghdad Science Journal
Determination of Advanced Oxidation Protein Products, E3 SUMO-Protein Ligase NSE2[NSMCE2], as a Marker to Predict Child Acute Lymphoblastic Leukemia
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Acute lymphoblastic leukemia (ALL) is a cancer of the blood and bone marrow (spongy tissue in the center of bone). In ALL, too many bone marrow stem cells develop into a type of white blood cell called lymphocytes. These abnormal lymphocytes are not able to fight infection very well. The aim of this study was to investigate possible links between E3 SUMO-Protein Ligase NSE2 [NSMCE2] and increase DNA damage in the childhood patients with Acute lymphoblastic leukemia (ALL). Laboratory investigations including hemoglobin(Hb) ,white blood cell (WBC) , serum total protein , albumin ,globulin , in addition to serum total antioxidant activity (TAA) , Advanced oxidation protein products(AOPP) and E3 SUMO-Protein Ligase NSE2[NSMCE2]. Blood samples

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Publication Date
Wed May 12 2021
Journal Name
Annals Of The Romanian Society For Cell Biology
The Speed and Direction of the Ball's Rotation and its Relationship to the Accuracy of the Front and Rear Side Longitudinal Blow in Wheelchair Tennis Players.
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The study aimed to identify the relationship between the speed and direction of the ball's rotation in the accuracy of the front and rear side longitudinal blow in wheelchair tennis players. The descriptive approach wasused in the manner of correlations to suit the nature of the problem to be studied. The research community identified the 32 players aged18 and over, and the search sample was selected from players with a local classification registered with the 2020 Wheelchair Ground Tennis Federation (2020) in the intentional manner of 8 players, using Smart Tennis Sensor technology to measure the speed and direction of the ball and test the accuracy of the front and rear side longitudinalstraightstrike. She conducted the reconnaissance exp

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Publication Date
Fri Mar 01 2024
Journal Name
وقائع المؤتمر العلمي العاشر لكلية اللغات
Picaresque Elements in Selected English and Iraqi Novels: A Comparative Approach عناصر رواية التشرد والرحلة على الطريق في روايات انكليزية وعراقية مختارة: دراسة مقارنة
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The paper attempts to find out the elements of picaresque novel in selected English and Iraqi novels. It studies these elements in Henry Fielding’s Joseph Andrews and Adil Abduljabbar’s Arzal Hamad Al-Salim. The paper is divided into four sections. The first is an introduction to the picaresque novel. It gives a definition, a historical background, and the elements of the genre. The second section studies Fielding’s novel focusing on the elements of this type of novel and how it affects the story itself. The paper follows the novel from the beginning to the end showing these elements. The third is dedicated to Abduljabbar’s novel and how the elements of picaresque genre appear in the novel and play an important role in its developm

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Publication Date
Wed Jun 01 2016
Journal Name
Journal Of Engineering
Management Model for Evaluation and Selection of Engineering Equipment Suppliers for Construction Projects in Iraq
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Engineering equipment is essential part in the construction project and usually manufactured with long lead times, large costs and special engineering requirements. Construction manager targets that equipment to be delivered in the site need date with the right quantity, appropriate cost and required quality, and this entails an efficient supplier can satisfy these targets. Selection of engineering equipment supplier is a crucial managerial process .it requires evaluation of multiple suppliers according to multiple criteria. This process is usually performed manually and based on just limited evaluation criteria, so better alternatives may be neglected. Three stages of survey comprised number of public a

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Publication Date
Thu Feb 07 2019
Journal Name
Journal Of The College Of Education For Women
Russian politics and geographical variable fixed in under the geostrategic changes (A study in the geo-political perspective and geopolitics)
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The purpose of this study is to show the constants and variables geography in Russian
policy in light of variables geostrategic witnessed by the world, especially after the collapse
of the Soviet Union and the disintegration to fifteen Republic became the Russian Federation
and the heir to the Soviet Union, Geography particularly important because the impact of its
data in policy making less change ofothers, and explain the political choices cannot achieve
security through its relationship constants geographical (natural or human) paint forms of
economic activity and determine the points they national security. issue is the geographical
this or that country is determined by its policy also specifies the way in which

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Publication Date
Fri Oct 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The role of internal marketing in achieving customer satisfaction An exploratory study of a sample of private bank managers in Baghdad
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This study examined the effect of elements of internal marketing activities on customer satisfaction through an exploratory study of banking services in the city of Baghdad, if the research problem crystallized by asking a group of questions, the most important (is there a correlation and impact between the dimensions of internal marketing and customer satisfaction, this study aims to determine The effect of internal communication, training and internal market research on customer satisfaction, represented by the quality of service, loyalty and market share, and embodied the objective of this study to identify the level of availability of internal marketing activities and programs in the research banks, data were collected using

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Publication Date
Sun Mar 01 2026
Journal Name
Journal Of Baghdad College Of Dentistry
A Study the Effect of Addition of Silanized Zirconium Oxide Nanoparticles on Some Properties of High-Impact Heat-Cured Acrylic Resin
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Background: The incorporation of rubber has not been entirely successful because it can have detrimental effects on the transverse Strength and hence the rigidity of the denture base. Materials and methods: Zirconium oxide nanoparticales were coated with a layer of trimethoxysilylpropylmethacrylate (TMSPM) before sonication in monomer (MMA) with the percentages 3% by weight then mixed with powder using conventional procedure.(100) samples were prepared and divided into five groups according to the test performed ,Each group consisted of 20 specimens and these were subdivided into 2 groupsGroup (A): control group (10 specimens of high impact acrylic resin without zirconium oxide) and Group (B):zirconium oxide group(10 specimens of high impac

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Publication Date
Thu Dec 15 2022
Journal Name
Al Kut Journal Of Economics And Administrative Sciences
The relationship of demographic diversity to institutional effectiveness An analytical study of a sample of workers in public organizations in Iraq
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Diversity has become one of the required phenomena to be available within public organizations, in light of the changes taking place in the global and international environment and in various fields. Therefore, it was imperative to study the impact of this phenomenon in various institutions, especially public ones, in most developing countries, including Iraq. The current research aims to analyze the relationship between The demographic diversity and institutional effectiveness of a sample of workers in public institutions included (500) respondents. The questionnaires were distributed to them randomly. Diversity is considered an independent variable and institutional effectiveness a dependent variable. The researcher used interview tools a

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