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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 Dec 15 2022
Journal Name
Engineering, Technology & Applied Science Research
Numerical Modeling of a Pile Group Subjected to Seismic Loading Using the Hypoplasticity Model
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Various simple and complicated models have been utilized to simulate the stress-strain behavior of the soil. These models are used in Finite Element Modeling (FEM) for geotechnical engineering applications and analysis of dynamic soil-structure interaction problems. These models either can't adequately describe some features, such as the strain-softening of dense sand, or they require several parameters that are difficult to gather by conventional laboratory testing. Furthermore, soils are not completely linearly elastic and perfectly plastic for the whole range of loads. Soil behavior is quite difficult to comprehend and exhibits a variety of behaviors under various circumstances. As a result, a more realistic constitutive model is

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Publication Date
Thu Jun 04 2020
Journal Name
Fibers
A Comparative Study of the Performance of Slender Reinforced Concrete Columns with Different Cross-Sectional Shapes
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Most reinforced concrete (RC) structures are constructed with square/rectangular columns. The cross-section size of these types of columns is much larger than the thickness of their partitions. Therefore, parts of these columns are protruded out of the partitions. The emergence of columns edges out of the walls has some disadvantages. This limitation is difficult to be overcome with square or rectangular columns. To solve this problem, new types of RC columns called specially shaped reinforced concrete (SSRC) columns have been used as hidden columns. Besides, the use of SSRC columns provides many structural and architectural advantages as compared with rectangular columns. Therefore, this study was conducted to explain the structura

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Publication Date
Tue Feb 04 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
A Comparative Study on the Probability of Diabetes and Psychosocial Deficiency of Badminton Players Youth Category
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Many people believe that diabetes appears after a psychological crisis, which is a misconception but it could be in them before having a crisis ore the crisis. But emotion increases the appearance of symptoms, and athletes are at risk of developing diabetes. Hypoglycemia is not unusual for athletes, and during physical activity the sugar level changes in the blood. Therefore, it is important to conduct tests for the measurement of sugar before and immediately after the activity, for the purpose of detecting the sharp drop in the sugar level and treating it, and the early detection is necessary to avoid the possibility of diabetes, the concept of psychological immunity in psychology is considered a positive concepts that maintain the balance

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Publication Date
Sat Dec 17 2022
Journal Name
Applied Sciences
A Hybrid Artificial Intelligence Model for Detecting Keratoconus
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Machine learning models have recently provided great promise in diagnosis of several ophthalmic disorders, including keratoconus (KCN). Keratoconus, a noninflammatory ectatic corneal disorder characterized by progressive cornea thinning, is challenging to detect as signs may be subtle. Several machine learning models have been proposed to detect KCN, however most of the models are supervised and thus require large well-annotated data. This paper proposes a new unsupervised model to detect KCN, based on adapted flower pollination algorithm (FPA) and the k-means algorithm. We will evaluate the proposed models using corneal data collected from 5430 eyes at different stages of KCN severity (1520 healthy, 331 KCN1, 1319 KCN2, 1699 KCN3 a

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Publication Date
Mon Oct 07 2019
Journal Name
Construction Innovation
A hybrid conceptual model for BIM in FM
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Purpose

The purpose of this paper is to develop a hybrid conceptual model for building information modelling (BIM) adoption in facilities management (FM) through the integration of the technology task fit (TTF) and the unified theory of acceptance and use of technology (UTAUT) theories. The study also aims to identify the influence factors of BIM adoption and usage in FM and identify gaps in the existing literature and to provide a holistic picture of recent research in technology acceptance and adoption in the construction industry and FM sector.

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Publication Date
Wed Jun 11 2008
Journal Name
Journal Of Al-nahrain University
ANALYSIS OF A MOLECULAR DYNAMICS SIMULATION OF THE ACETYLCHOLINESTERASE ENZYME AND ITS COMPLEX WITH (AXILLARIDINE-A) INHIBITOR
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Molecular dynamics (MD) simulations were carried out in order to investigate the binding mode of axillaridine-A at the active site of human acetylcholinesterase (AChE) enzyme. 2.0 nanosecond of MD simulations was made for the protein and the complex to dynamically explore the active site and the behavior of the ligand at the peripheral AChE binding site. These calculations for the enzyme alone showed that the active site of AChE is located at the bottom of a deep and narrow cavity whose surface is lined with rings of aromatic residues and Tyr72 is almost perpendicular to the Trp286 ring and forms a stable - interaction. The size of the active site of the complex decreases with time due to increase the interaction. Axillaridine-A forms

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Publication Date
Mon Mar 23 2020
Journal Name
Baghdad Science Journal
Surfactant Cloud Point Extraction as a Procedure of Preconcentrating for Metoclopramide Determination Using Spectro Analytical Technique
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In current article an easy and selective method is proposed for spectrophotometric estimation of metoclopramide (MCP) in pharmaceutical preparations using cloud point extraction (CPE) procedure. The method involved reaction between MCP with 1-Naphthol in alkali conditions using Triton X-114 to form a stable dark purple dye. The Beer’s law limit in the range 0.34-9 μg mL-1 of MCP with r =0.9959 (n=3) after optimization. The relative standard deviation (RSD) and percentage recoveries were 0.89 %, and (96.99–104.11%) respectively. As well, using surfactant cloud point extraction as a method to extract MCP was reinforced the extinction coefficient(ε) to 1.7333×105L/mol.cm in surfactant-rich phase. The small volume of organi

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Publication Date
Tue Sep 28 2021
Journal Name
Journal Of The College Of Education For Women
An Estimated Answer of a Condition between the Interpretive Structure and Surface Structure: Al-Qurtubi’s Tafseer as a Model: عمر عقلة خليف الدعجة
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This present work is concerned with one of the syntactic issues that has been researched by many linguists, grammarians, and specialists in Islamic studies, the estimated answer to a condition. However, this topic is researched this time by examining Imam Al-Qurtbi’s opinions in interpreting related ayas from the holly Quraan in his book (Collector of Quranic Rules) or its transliteration (Al-Jami’ Li Ahkam Al-Quran). Such a step involves commenting on, tracking what Al-Qurtbi said in this regard, discussing it from the points of view of other grammarians, and judging  it accordingly, taking into account the apparent surface structures of the examples collected. To achieve this objective, the inductive analytical approach has be

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Publication Date
Mon May 18 2026
Journal Name
Al–bahith Al–a'alami
Preferences of the Iraqi Public towards Arab News Channels Programs and Materials (Al Jazeera, Al Arabiya, Al Ekhbariya Satellite Channels: a field Study)
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Broadcasting across satellites has become an important media phenomenon and largely available for watchers. As the receiver can see the events at the very moment and at any spot in the world. This study aims to discover the degree of the extent of exposure of Iraqi people to the news broadcasting satellites in Arabic language, (Al Jazeera, Al Arabiya, Al Ekhbariya Satellite Channels) as one of the media that serves the public; and to discover the range of these Satellite Channels in covering the local Iraqi situation in different sides and aspects; and to know the significance of the Iraqi people in watching those news programmers; and state the motives behind the Iraqi public's dependence on these channels.

The

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Publication Date
Tue Apr 18 2023
Journal Name
Al–bahith Al–a'alami
Public relations programs and its role to enhance the morale of employees in the Ministry of Transportation: A survey study on the State land Transport Company
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This research aims to learn about public relations programs and their role to enhance the morale of the State land Transport Company employees.The researcher relied on the survey method and use a questionnaire and scale tools to collect information from workers in the Department of Relations and Media and employees in all departments.
The research reached several conclusions, including:
1- Public relations seek to increase workers’ confidence in senior management and motivate them to improve their production, as well as their relentless endeavor to bring workers closer by following multiple and varied forms of communication with them.
2- The results of the study showed that there was a negative i

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