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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
Wed Jul 17 2019
Journal Name
Aip Conference Proceedings
The correction of the line profiles for x-ray diffraction peaks by using three analysis methods
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In this study used three methods such as Williamson-hall, size-strain Plot, and Halder-Wagner to analysis x-ray diffraction lines to determine the crystallite size and the lattice strain of the nickel oxide nanoparticles and then compare the results of these methods with two other methods. The results were calculated for each of these methods to the crystallite size are (0.42554) nm, (1.04462) nm, and (3.60880) nm, and lattice strain are (0.56603), (1.11978), and (0.64606) respectively were compared with the result of Scherrer method (0.29598) nm,(0.34245),and the Modified Scherrer (0.97497). The difference in calculated results Observed for each of these methods in this study.

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Publication Date
Tue Oct 11 2022
Journal Name
College Of Islamic Sciences
The Jurisprudence rule and its impact on Islamic legislation “Forcing does not nullify the rights of others” as a model .
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Research Summary :

         Praise be to God, Lord of the Worlds, and prayers and peace be upon the Master of the Messengers, his family and all his companions, then after:

     This is brief research that contained between its two covers one of the jurisprudence rules derived from Islamic Sharia that guarantees the right of others, in case of forcing to do the prohibited act, and it is a restriction of the rule: “Necessities allow prohibitions” and “Hardship brings facilitation” and support for the rule: “Necessities are valued.” It is an origin in alleviating the taxpayer definitely , and the study has briefly shown some of the jurisprudential appli

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Publication Date
Tue Jan 01 2008
Journal Name
J Bagh College Of Dentistry
A comparative study of the sealing ability of two different obturation techniques with and without the use of sealers.
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Background: The final stage of endodontic therapy is complete obturation of the root canal system to provide as perfect as possible at the cementodentinal junction of the apical foramen. The purpose of this in vitro study was to evaluate the sealing ability of injection molded thermoplasticized gutta percha and lateral condensation techniques with and without the use of sealers. Materials and Methods: Forty freshly extracted adult human maxillary central incisors with complete formed apices were utilized in this study. The teeth were randomly divided into four groups for evaluation of the apical seal. Group (1) lateral condensation gutta percha technique without sealer, (2) lateral condensation gutta percha technique with sealer, (3) Inject

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Publication Date
Tue Jun 15 2021
Journal Name
Al-academy
The concept of freedom in the texts of Yashar Kamal play "The play (The Plate) as a model": عامر صباح نوري المرزوك
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This research is concerned with studying (the concept of freedom in the texts of Yaşar Kamal the play), as the Turkish playwright (Kamal Yasar) is one of the contemporary playwrights who have been interested in and criticize society, and perhaps the concept of freedom in his texts took a different form, through his ability to renew and present his attempts to create A theatrical form different from his earlier writers in dealing with the life of the peasants and the oppression that went through them, as the researcher identified the problem of his research with the following question: What is the concept of freedom in the texts of Yashar Kamal? The research aims to define the concept of freedom in the texts of Yashar Kamal of the play,

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Publication Date
Tue Dec 30 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Immunohistochemical expression of MMP1 and TIMP1 as markers of migration in Hodgkin’s and non-Hodgkin’s lymphoma of the head and neck region (A comparative study)
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Background: Malignant lymphoma is a term that describes primary tumors of the lymphoreticular system, almost all of which arise from lymphocytes.MMP-1 is the most ubiquitously expressed interstitial collagenase, a subfamily of MMPs that cleaves stromal collagens. It is also called collagenase-1.TIMPs which inhibits MMP activity and thereby restrict extracellular matrix breakdown, TIMP-1 is a stromal factor that has a wide spectrum of functions in different tissues. Material and Methods: This study was performed on (68) formalin-fixed, paraffin-embedded blocks, histopathologically diagnosed as lymphoma (head and neck lesions). Immunohistochemical staining of MMP1and TIMP1 was performed on each case of the study sample. Results: The expressio

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Publication Date
Thu Mar 30 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Spectroscopic Study for Determination of Amoxicillin Using Cobalt(II) as Complexing Metal
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         This study includes analytical methods for the determination of the drug amoxicillin trihydrate (Amox.) in some pharmaceutical preparations using Cobalt ion (Co(II)) as complexing metal. The best conditions for complexation were: the reaction time was 20 minutes, pH=1.5 and the best temperature of reaction was 70 ËšC. Benzyl alcohol was the best solvent for extraction the complex.

Keywords: Amoxicillin, Cobalt(II), Complex, Molar ratio.

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Publication Date
Tue Jan 01 2019
Journal Name
Therapeutic Advances In Drug Safety
Deferasirox in thalassemia: a comparative study between an innovator drug and its copy among a sample of Iraqi patients
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Background:

The health care industry is witnessing an increasing trend in the use of generic medicines because of their presumed low cost compared with innovator medicines. The aim of this study was to determine and compare the performance of the copy drug Osveral®and its innovator drug deferasirox (Exjade®).

Methods:

A prospective observational study including 223 patients receiving the branded medicine Exjade®and 101 patients receiving the copy Osveral®was carried out. Data were assessed for a 1-year period and included clinical symptoms, serum ferrit

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Publication Date
Mon Jan 01 2024
Journal Name
Aip Conference Proceedings
A multivariate Bayesian model using Gibbs sampler with real data application
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In many scientific fields, Bayesian models are commonly used in recent research. This research presents a new Bayesian model for estimating parameters and forecasting using the Gibbs sampler algorithm. Posterior distributions are generated using the inverse gamma distribution and the multivariate normal distribution as prior distributions. The new method was used to investigate and summaries Bayesian statistics' posterior distribution. The theory and derivation of the posterior distribution are explained in detail in this paper. The proposed approach is applied to three simulation datasets of 100, 300, and 500 sample sizes. Also, the procedure was extended to the real dataset called the rock intensity dataset. The actual dataset is collecte

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Publication Date
Tue Jun 01 2021
Journal Name
Al-khwarizmi Engineering Journal
Effect of Environmental Factors on the Accuracy of a Quality Inspection System Based on Transfer Learning
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In this research, a study is introduced on the effect of several environmental factors on the performance of an already constructed quality inspection system, which was designed using a transfer learning approach based on convolutional neural networks. The system comprised two sets of layers, transferred layers set from an already trained model (DenseNet121) and a custom classification layers set. It was designed to discriminate between damaged and undamaged helical gears according to the configuration of the gear regardless to its dimensions, and the model showed good performance discriminating between the two products at ideal conditions of high-resolution images. So, this study aimed at testing the system performance at poo

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Publication Date
Tue Jun 01 2021
Journal Name
Al-khwarizmi Engineering Journal
Effect of Environmental Factors on the Accuracy of a Quality Inspection System Based on Transfer Learning
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In this research, a study is introduced on the effect of several environmental factors on the performance of an already constructed quality inspection system, which was designed using a transfer learning approach based on convolutional neural networks. The system comprised two sets of layers, transferred layers set from an already trained model (DenseNet121) and a custom classification layers set. It was designed to discriminate between damaged and undamaged helical gears according to the configuration of the gear regardless to its dimensions, and the model showed good performance discriminating between the two products at ideal conditions of high-resolution images.

So, this study aimed at testing the system performance at poor s

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