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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 Jul 12 2024
Journal Name
World Water Policy
The effect of natural factors on changing soil uses in the marshes: An experimental study using Landsat satellite data
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The study aimed to analyze the effect of meteorological factors (rainfall rate and temperature) on the change in land use in the marshes of the Al‐Majar Al‐Kabir region in southern Iraq. Satellite images from Landsat 7 for 2012 and Landsat 8 for 2022 were used to monitor changes in the land coverings, the images taken from the Enhanced Thematic Mapper Plus (ETM+) and Operational Land Imager (OLI) sensors of the Landsat satellite. Geometric correction was used to convert images into a format with precise geographic coordinates using ArcMap 10.5. The maximum likelihood classification method was used to examine satellite image data using a supervised approach, and the data were analyzed statistically. We obtained clear images of the area,

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Publication Date
Sat Oct 28 2023
Journal Name
Baghdad Science Journal
Lead acetate deteriorates the improvement effect of L-arginine and tetrahydrobiopterin on endothelin-1 receptors activity in rat aorta
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Endothelin-1 (ET-1) is a potent vasoconstrictor hormone that has been identified as an important factor
responsible for the development of cardiovascular dysfunctions. ET-1 exerts its vasoconstrictor activity
through two pharmacologically distinct receptors, ETA and ETB that are found in vascular smooth muscle
cells (VSMCs) and the vasodilator activity through an ETB receptor located on endothelial cells. This study
aimed to show the impact of 1µM L-arginine (LA), 100µM tetrahydrobiopterin (BH4), and their combined
effect on ET-1 activity in both lead-treated and lead-untreated rat aortic rings. This means, investigating how
endothelial dysfunction reverses the role of nitric oxide precursor and cofa

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Publication Date
Sun Jun 30 2019
Journal Name
Journal Of The College Of Education For Women
Qualities of Life Partner from the Perspective of a Sample of University Students
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The study aims at identifying the morphological and psycho-socio-economic qualities wished to be in a life partner among a sample of Palestinian youth. The total sample was (231) and consisted of  (83) male and (148) female students. Each student presented a detailed report on the qualities he/she wished to be in life partner. The study used the descriptive approach and content analysis method. The validity and stability of the analysis were calculated. The results showed eight qualities in both groups: physical, psychological, emotional, social, intellectual, familial, economic and academic. Female students were found to have more variations than male students in terms of the qualities preferable in the life partner. Male students

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Publication Date
Wed Sep 15 2021
Journal Name
Al-academy
Exposure and its working mechanisms in theatrical multi-scene model "critical dramaturgy study": يوسف رشيد جبر
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The concept of intertextuality was one of the problems that occupied the attention of critics and critics in targeting the structure of textual intertextuality between texts and their overlap in the process of producing meaning. Until intertextuality became a stable term and it can be monitored in the structure of the theatrical text and determining the mechanisms of this intertextuality between texts through fields and classifications agreed upon by the most important critics who wrote and considered intertextuality. Perhaps our previous research (the approach of exposure in the epistemological hallway to intertextuality) was an attempt to interview a terminology, which the researcher intended to monitor, through the mechanisms of inter

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Preparation of superposed thin film (CdTe)1-xSex / ZnS and Studying the Effect of Concentration on Some its Electrical Properties.
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Preparation of superposed thin film (CdTe)1-xSex / ZnS) with concentration of (x= 0.1, 0.3, 0.5) at a temperature of substrate (Ts= 80 0C) by using Thermal Vacuum Evaporation System. The measurement of X-ray diffraction shows that the compounds CdTe, ZnS, (CdTe)1-xSex and (CdTe)1-xSex / ZnS have a polycrystalline structure, the C-V characteristic shows that the capacitance degrease by increasing the concentration (x) in reverse bias, while the I-V characteristic shows the current dark (Id) increase in forward and reverse bias by increasing (x) and the photocurrent (Iph) increase in reverse bias by increasing the concentration (x), the values of photocurrent are greater than from the values of the dark current for all concentrations

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Publication Date
Wed Mar 01 2023
Journal Name
International Journal Bioautomation
Photobiomodulation Effect of 850 nm Near-infrared Diode Laser on the Release of M1-related Cytokines Inmonocytic THP-1 Cells
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Photobiomodulation (PBM) is a form of the use of visible red and Near-infrared (NIR) light at low power, where a laser light photon is absorbed at the electronic level, without heat production. PBM can be applied in wide range of treatment to help the wound, inflammation, edema, and pain reduction. However, there is a lack of scientific documentation regarding its actual effects. Objectives: This study assesses the impact of PBM on the release of M1-related cytokine in monocyte cells with particular emphasis on interleukin-1β (IL-1β) and Tumour Necrosis Factor α (TNF-α). Methods: Tamm-Horsfall Protein 1 (THP-1) macrophages M1 cells have been exposed to the light from the diode laser of 850nmat different doses (0, 0.6, 1.2 and 3.

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Publication Date
Sun Jun 02 2019
Journal Name
Baghdad Science Journal
Effect of Dopant Concentration on the Structural, Optical and Sensing Properties of (SnO2)1-x(TiO2:CuO)x Sprayed Films
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      Spray pyrolysis technique was subjected to synthesized (SnO2)1-x (TiO2: CuO) x Thin films on different substrates like glass and single crystal silicon using. The structure of the deposited films was studied using x-ray diffraction. A more pronounced diffraction peaks of SnO2 while no peaks of (CuO , TiO2 ) phase appear in the X-ray profiles by increasing of the content of (TiO2 , CuO) in the sprayed films. Mixing concentration (TiO2 , CuO) influences on the size of the crystallites of the SnO2 films ,the size of crystallites of the spray paralyzed oxide films change in regular manner by increasing of (TiO

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Publication Date
Sun Nov 01 2015
Journal Name
Journal Of Dentistry
New functional and aesthetic composite materials used as an alternative to traditional post materials for the restoration of endodontically treated teeth
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Objectives To tailor composites of polyethylene–hydroxyapatite to function as a new intracanal post for the restoration of endodontically treated teeth (ETT). Methods Silanated hydroxyapatite (HA) and zirconium dioxide (ZrO2) filled low-density polyethylene (LDPE) composites were fabricated by a melt extrusion process and characterised using infrared spectroscopy (FTIR), differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA). The flexural strength and modulus were determined in dry state and post ageing in simulated body fluid and fractured surfaces analysed by SEM. The water uptake and radiographic appearance of the experimental composites were also measured and compared with a commercially known endodontic fibre

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Publication Date
Fri Jan 01 2016
Journal Name
Journal Of Computer And Communications
Parallel Quick Search Algorithm for the Exact String Matching Problem Using OpenMP
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String matching is seen as one of the essential problems in computer science. A variety of computer applications provide the string matching service for their end users. The remarkable boost in the number of data that is created and kept by modern computational devices influences researchers to obtain even more powerful methods for coping with this problem. In this research, the Quick Search string matching algorithm are adopted to be implemented under the multi-core environment using OpenMP directive which can be employed to reduce the overall execution time of the program. English text, Proteins and DNA data types are utilized to examine the effect of parallelization and implementation of Quick Search string matching algorithm on multi-co

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Publication Date
Tue Mar 01 2022
Journal Name
The International Journal Of Nonlinear Analysis And Applications
Improved optimality checkpoint for decision making by using the sub-triangular form
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Decision-making in Operations Research is the main point in various studies in our real-life applications. However, these different studies focus on this topic. One drawback some of their studies are restricted and have not addressed the nature of values in terms of imprecise data (ID). This paper thus deals with two contributions. First, decreasing the total costs by classifying subsets of costs. Second, improving the optimality solution by the Hungarian assignment approach. This newly proposed method is called fuzzy sub-Triangular form (FS-TF) under ID. The results obtained are exquisite as compared with previous methods including, robust ranking technique, arithmetic operations, magnitude ranking method and centroid ranking method. This

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