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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 Sep 07 2008
Journal Name
Baghdad Science Journal
A Study of some biochemical parameters in patients with - thalassemia
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Serum levels of iron,copper,ceruloplasmin and transferrine were estimated in three groups of patients with ?- thalassemia: 24 patients have splenectomy thalassemia major, 29 patients have non splenectomy thalassemia major and 19 patients have thalassemia intermedia , data were compared to normal and pathological controls (anemia and minor). There were significant increase in trace element levels in all studied groups of pateints as compared to normal and pathological controls. Also there were a significant increase in ceruloplasmin levels,While the result revealed that there were a significant decrease in transferrine levels in all groups of patients studied as compared to normal and pathological controls. The result also indicate that the

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Publication Date
Thu Nov 01 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Life – Style of patients with peptic ulcer A case control study
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Abstract A descriptive (retrospective) (a case-control) study was carried out at Al-Karama Teaching Hospital, Baghdad Teaching Hospital and Surgical Specialties Hospital, and Gastro-Intestinal Tract and Liver (GIT) Hospital for the period of December 1st, 2001 To March 15th 2002. To identify aspects of life-style that may contribute to the occurrence of peptic ulcer (P.U)as risk factors. And to find out the relationship between the demographic characteristic of the group. Non-probability (Purposive) sample of (100) cases who were admitted to the endoscopy department who were later on diagnosed as having

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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
A Cognitive Linguistic Study of UP and DOWN in Iraqi Arabic
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This study is an attempt to investigate the conceptual metaphor of UP and DOWN commonly used in Iraqi community. Some of the metaphorical expressions in Iraqi colloquial Arabicarewidely used by Iraqi speakers in everyday language. Ithas been analyzed by following the cognitive theory of metaphor (Lakoff& Johnson,1980).The study indicates that the Iraqi speakerexperiences more of the metaphorical expressions of UP and DOWN to referto many of the abstract concepts that shape his/her impression of everyday life situations.

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Publication Date
Thu Dec 15 2022
Journal Name
Arab World English Journal
Genre-Based Analysis of Selected Political Debates: A Discourse Analysis Study
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The researchers of the present study have conducted a genre analysis of two political debates between American presidential nominees in the 2016 and 2020 elections. The current study seeks to analyze the cognitive construction of political debates to evaluate the typical moves and strategies politicians use to express their communicative intentions and to reveal the language manifestations of those moves and strategies. To achieve the study’s aims, the researchers adopt Bhatia’s (1993) framework of cognitive construction supported by van Emeren’s (2010) pragma-dialectic framework. The study demonstrates that both presidents adhere to this genre structuring to further their political agendas. For a positive and promising image

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Publication Date
Wed Sep 28 2022
Journal Name
Journal Of The College Of Education For Women
A Cognitive Linguistic Study of Battered Woman in Selected Iraqi Caricatures
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The present paper is a qualitative descriptive study. It aims to examine the macro-cultural schemata addressing the concept of violence against women in Iraq from a cognitive linguistic point of view. To meet this objective, a number of Iraqi social caricatures have been selected from two popular and active Iraqi caricaturists, Odeh Al-Fahdawi and Nasser Ibrahim. The selection and the analysis of data have been achieved following the validity and reliability procedures and the ethical considerations. To meet this objective, Sharifian’s Model (2011) of Cultural Schemata has been adopted in data analysis. The study has concluded that the macro-cultural schemata regarding the concept of violence in the selected panels reveals that violenc

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Publication Date
Thu Sep 15 2022
Journal Name
Bionatura
Chronic Myeloid Leukemia: A retrospective study of clinical and pathological features
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Chronic myeloid leukemia (CML), is one of the myeloproliferative disorders with a characteristic cytogenetic abnormality resulting in the BCR-ABL fusion gene. Imatinib Mesylate is an effective agent for treating patients in all stages of CML. According to the annual Iraqi cancer registry 2019, the total number of chronic myeloproliferative disorders was 338. The percentage and incidence rates were 0.94% and 0.86%, respectively, with a higher incidence rate in males than females (1.12 in males and 0.60 in females). In this registry, no details about CML, so this study aimed to estimate the number of CML patients who attended the national center of hematology from 2005 until 2020 and investigate their epidemiological and clinic-pathol

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Publication Date
Thu Sep 30 2021
Journal Name
Rigeo
A Stylistic Study of Vocative Particles in Selected English Literary Texts
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A vocative expression can be defined as an expression of direct address where the participant identity is set forth explicitly within a sentence. This study aims at showing how the vocative particles are used in literally texts, namely in the short story “The Garden Party" written by Kathryn Mansfield and identifying the forms of these vocative particles as used by the characters along with the functions of these vocative particles. For the analysis of vocative forms, the researcher used Quirk and Greenbaum (1973) model. Functionally, the data were analyzed based on Quirk et al. (1985) model. However, the results of this study shows that the characters in “The Garden Party” short story used various forms of vocative particles and

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Publication Date
Thu Aug 05 2021
Journal Name
International Journal Of Renewable Energy Development
Desalination of Agricultural Wastewater by Solar Adsorption System: A Numerical Study
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There are still areas around the world suffer from severe shortage of freshwater supplies. Desalination technologies are not widely used due to their high energy usage, cost, and environmental damaging effects. In this study, a mathematical model of single-bed adsorption desalination system using silica gel-water as working pair is developed and validated via earlier experiments. A very good match between the model predictions and the experimental results is recorded. The objective is to reveal the factors affecting the productivity of fresh water and cooling effect in the solar adsorption system. The proposed model is setup for solving within the commercially-available software (Engineering Equation Solver). It is implemented to so

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Publication Date
Mon Sep 04 2017
Journal Name
Journal Of College Of Education For Women
Tagmemic Analysis of English and Arabic Praise Poetry: A Contrastive Study
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This research provides a new method to study praise poetry that can be used as a course to teach English and Arabic to students in the College of Education. This research answers two questions: Is it possible to examine praise poetry as a tagmeme? Is this analysis of great help in teaching English and Arabic to students in the College of Education? The data that will be chosen for the purpose of analysis are two of Shakespeare's sonnets and two of AL Mulik's poems. The sonnets selected for this purpose are 17 and 18. AL Mulik's poems selected for the same purpose are 8 and 9. Each line in both English and Arabic data is numbered by the researcher herself. Then, those lines are grouped into sentences to facilitat

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Publication Date
Thu Feb 07 2013
Journal Name
Iraqi Journal Of Medical Science
A study of serum magnesium and calcium levels in missed abortion
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