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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
Tue Mar 28 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Study the Effect of Folic Acid as A supplement on Selected Oxidative Stress and Biochemical Parameters in First Trimester of Pregnancy
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Folic acid modulates several disorders in humans, pregnancy mostly because of the mitochondria-rich placenta, is a condition that favors oxidative stress.Transitional metals, especially iron, which are particularly abundant in the placenta, are important in the production of free radicals. Adenosine deaminase (ADA), an enzyme essential for the differentiation of lymphoid cells, has been used for monitoring diseases with altered immunity. In the present study we investigated the effect of regular and irregular administered folic acid in the first and second trimester of pregnancy to be compared with non-pregnant women ,and also the effect of regular and irregular using of folic acid  supplement on  oxidative stress parameters an

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Publication Date
Mon Nov 19 2018
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Comparison Study of the Effect of Erlotinib as a Tyrosine Kinase Inhibitor on Electrolyte Levels in Type2 Diabetic and Diabetic Nephropathy
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Diabetes mellitus can be defined as  a metabolic disorder disease .Complication  of diabetes  are due to diabetic nephropathy .This study was done in vitro to study the effect of different concentrations of erlotinib inhibitor ( tyrosine kinase inhibitor) on electrolyte levels (Mg⁺²,Ca⁺²,Na⁺) in sera of Iraqi patients with  newly diagnosis type2 diabetes and diabetic nephropathy in addition to find the best percentage inhibition for utilizing different concentrations from erlotinib (6.97x10⁻⁷, 9.30x10⁻⁷ ,1.16x10⁻⁶,1.39x10⁻⁶ ,1.62x10⁻⁵ )molar  on electrolyte levels . This study was conducted in The National Diabetes Ce

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Publication Date
Thu Dec 15 2022
Journal Name
Al-adab Journal
Metaphors and comparisons as a means of rethinking the phenomena of the surrounding world
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The article characterizes metaphors and comparisons as a means of rethinking the phenomena of the surrounding world; two directions are named within which metaphors and comparisons are studied: 1) the linguo-classification direction combines several classifications of metaphors and comparisons, which are basically focused on comparing two denotations through the meanings of word forms that are part of the trope; 2) the theoretical and conceptual direction is associated with the concept of conceptual displacement and is the basis of the theoretical and methodological study of metaphor and comparison, i.e. the modern theory of metaphor is being formed; The main attention is focused on the comparative concept of Aristotle, which postul

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Publication Date
Thu Oct 01 2020
Journal Name
Journal Of Engineering
Developing a Model to Estimate the Productivity of Ready Mixed Concrete Batch Plant
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Productivity estimating of ready mixed concrete batch plant is an essential tool for the successful completion of the construction process. It is defined as the output of the system per unit of time. Usually, the actual productivity values of construction equipment in the site are not consistent with the nominal ones. Therefore, it is necessary to make a comprehensive evaluation of the nominal productivity of equipment concerning the effected factors and then re-evaluate them according to the actual values.

In this paper, the forecasting system was employed is an Artificial Intelligence technique (AI). It is represented by Artificial Neural Network (ANN) to establish the predicted model to estimate wet ready mixe

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Publication Date
Wed Jul 01 2015
Journal Name
Political Sciences Journal
The concept of ethnicity in contemporary American political thought Jerry Mueller, a model ...
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الخلاصة

تشير نظريات علم اجتماع المعرفة الى ان ظهور مفهوم معين او سقوطه لايتم بمحض الصدفة، بل نتيجة تفاعل مجموعة من العوامل الثقافية والسياسية وحتى الاقتصادية ومن هنا فأن ظهور مفهوم الاثنية كان محصلة عوامل كثيرة خصوصاً بعد ان اصبح موضوع الاثنية في العقود الاخيرة من القرن الماضي وبداية القرن الواحد والعشرين محور نقاش رئيس في ميدان البحث الاجتماعي والسياسي، ليس في

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Publication Date
Fri Jan 20 2023
Journal Name
Ibn Al-haitham Journal For Pure And Applied Sciences
Estimation of a Parallel Stress-strength Model Based on the Inverse Kumaraswamy Distribution
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 The reliability of the stress-strength model attracted many statisticians for several years owing to its applicability in different and diverse parts such as engineering, quality control, and economics. In this paper, the system reliability estimation in the stress-strength model containing Kth parallel components will be offered by four types of shrinkage methods: constant Shrinkage Estimation Method, Shrinkage Function Estimator, Modified Thompson Type Shrinkage Estimator, Squared Shrinkage Estimator. The Monte Carlo simulation study is compared among proposed estimators using the mean squared error. The result analyses of the shrinkage estimation methods showed that the shrinkage functions estimator was the best since

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Publication Date
Mon Jan 02 2017
Journal Name
Journal Of Educational And Psychological Researches
Toward a theoretical model of the terrorist personality and differentiation from psychopathic personality
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The current theoretical research targeted to construct a model of terrorist personality and its differentiation from psychopathic personality . Several assumptions or theories of perspectives of psychopathic personality have been compared with the terrorist personality studies that concerned . The suggested theoretical  model is interrupting the terrorist personality . The conclusions , discussions are mentioned. Finally, recommendation is suggested .

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Publication Date
Mon May 01 2017
Journal Name
The Journal Of Immunology
Resveratrol improves a murine model of asthma through alterations in the gut microbiome
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Abstract<p>Asthma is a condition characterized by bronchial spasms, inflammation, and mucous hypersecretion which leads to difficulties in respiration. Asthmatic patients are usually presented with recurrent attacks of coughing, wheezing, and shortness of breath which could be life-threatening. More than three million cases of asthma in the United States are diagnosed annually. Resveratrol, a polyphenolic stilbene, is known to be useful in controlling asthmatic attacks via different molecular mechanisms within the lung epithelium and infiltrating immune cells. However, few studies mentioned the effect of resveratrol on the microbiome in ovalbumin-induced asthma mouse model. In this study, we ind</p> ... Show More
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Publication Date
Tue Aug 01 2023
Journal Name
Baghdad Science Journal
A New Model Design for Combating COVID -19 Pandemic Based on SVM and CNN Approaches
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       In the current worldwide health crisis produced by coronavirus disease (COVID-19), researchers and medical specialists began looking for new ways to tackle the epidemic. According to recent studies, Machine Learning (ML) has been effectively deployed in the health sector. Medical imaging sources (radiography and computed tomography) have aided in the development of artificial intelligence(AI) strategies to tackle the coronavirus outbreak. As a result, a classical machine learning approach for coronavirus detection from      Computerized Tomography (CT) images was developed. In this study, the convolutional neural network (CNN) model for feature extraction and support vector machine (SVM) for the classification of axial

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Publication Date
Wed Feb 20 2019
Journal Name
Political Sciences Journal
US policy toward the political movement in the Arab countries Egypt a model
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The whole world and the Arab world, especially an important part of this international system, is undergoing a radical transformation at all levels. This mosaic of political, economic, social and military relations and alliances, whether based on the special interests of the major Powers or on the basis of mutual interests, The major transformations to social, economic, political and military conflict and these transformations still bear more surprises, at all levels, nothing remains constant, all changed, relations changed and alliances changed and loyalties fell and the principles of the M changed and the spectacular imperial economies collapsed and the will of the masses was no longer fixed.

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