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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 Apr 23 2021
Journal Name
Al-nahrain Journal Of Science
A Clinical-Statistical Study on COVID-19 Cases in Iraq: A Case Study
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Background: COVID-19 is a disease that started in Wuhan/China in late 2019 and continued through 2020 worldwide. Scientists worldwide continue to research to find vaccines, treatments, and medication for this disease. Studies also conenue to find the pathogenicity and epidemiology mechanisms. Materials and Methods: In this work, we analyzed cases obtained from Alshifaa center in Baghdad/Iraq for 23/2/2020-31/5/2020 with total instances of 797, positive cases of 393, and death cases of 30. Results: Results showed that the highest infection cases were among people aged between 41-45. Also, it was found that males' number of cases was more than females. In contrast, death cases were significantly higher in males than females. It was not

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Publication Date
Mon Jan 01 2024
Journal Name
Oncology And Radiotherapy
Comparting study of cytokeratin 18 fragment M65 with CA19-9 and CEA as a biomarker in Iraqi colon cancer patients
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Publication Date
Thu Oct 01 2020
Journal Name
The Asian Efl Journal
The Effect of Flow as a Strategy on EFL Student-teachers' Performance and their Flow
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This study aims at suggesting flow as a strategy for training female EFL student-teachers in the teaching training course and finding out the effect of this strategy on their performance and their flow state. The training course syllabuses will be constructed according to the flow nine factors and the teaching skills. The measurement tools are the student-teacher performance checklist that has already been used by the department of English language and SHORT Flow State Scale (S FSS-2). The study population is represented with the (60) female student-teachers/ fourth stage/ evening studies at theEnglish department /college of education for women/the University of Baghdad. The study is used the experimental design in that (30) of the student-

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Publication Date
Thu Aug 20 2020
Journal Name
Arab World English Journal
Investigating the Effectiveness of YouTube as a Learning Tool among EFL Students at Baghdad University
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YouTube is not just a platform that individuals share, upload, comment on videos; teachers and educators can utilize it to the best maximum so that students can have benefits. This study aims at investigating how active and influential YouTube can be in the educational process and how it is beneficial for language teachers to enhance the skills of students. The study demonstrates different theoretical frameworks that tackle the employment of technology to enhance the learning/teaching process. It relies on the strategies of Berk (2009) for using multimedia media, video clips in particular to develop the abilities of teachers for using technology in classrooms. To achieve the objective of the study, the researchers develop a questionnair

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Publication Date
Mon Mar 07 2022
Journal Name
Journal Of Educational And Psychological Researches
The Mental Disorder of mothers as a Mediating Variable Between Marital adjustment and Kindergarteners Development
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This current study aimed to explore the mediation effects of mother's mental health symptoms between marital adjustment and child development aspects. (666) participants of mothers and their children were the sample of the study. The researchers used the marital adjustment scale prepared by Manson, Morse, Lerner, Arthur, as well as, a package of tests for some aspects of growth Kindergarten children prepared by Kenawi and Mohamed (1999). In addition, theyemployed a list of modified symptoms (Symptom Checklist-90- Revised (SCL) -90-, prepared by Derogatis, Lipman and Lipogun & Cov (1976), The results of the current study showed there is a statistically significant relationship between marital adjustment and the symptoms of mental diso

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Publication Date
Sun Dec 30 2018
Journal Name
2018 Computing In Cardiology Conference (cinc)
Theoretical and Experimental Reflection Coefficients in Flexible Tubes as a Function of the Mach Number
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The standard formulation of Wave Intensity Analysis (WIA) assumes that the flow velocity (U) in the conduit is <;<; the velocity of propagation of waves (c) in the system, and Mach number, M=U/c, is negligible. However, in the large conduit arteries, U is relatively high due to ventricular contraction and c is relatively low due to the large compliance; thus M is > 0, and may not be ignored. Therefore, the aim of this study is to identify experimentally the relationship between M and the reflection coefficient in vitro. Combinations of flexible tubes, of 2 m in length with isotropic and uniform circular cross sectional area along their longitudinal axes, were used to present mother and daughter tubes to produce a range of reflection coeffic

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Publication Date
Fri Dec 01 2017
Journal Name
Iraqi Postgraduate Medical Journal
The polycystic ovary syndrome as a cause of increase in inflammatory markers and metabolic risks
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BACKGROUND: Polycystic ovary syndrome(PCOS) is one of the most common endocrine disorder affecting women in reproductive age. No single etiologic factor fully accounts for the spectrum of abnormalities in the polycystic ovary syndrome. Different changes in hormonal, metabolism and the inflammatory markers as squealy of PCOS with adverse effect on the women life. OBJECTIVE: To study the relationship between polycystic ovary syndrome and levels of C-reactive protein, human interleukin and hormonal and metabolic alteration in women with PCOS PATIENTS AND METHODS: Thirty women with Polycystic Ovary syndrome (PCOS) and other thirty women without PCOS were included. Venous blood samples were taken in early follicular phase of menstrual cycle [day

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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)
Some Variables Affecting the Formulation of Pentoxifylline (PTX) as a Solid Sustained Release Dosage Form
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An inert matrix  that is used to control the release of  (PTX) was prepared using Eudragit RL100 and RSPM types as matrix forming agent . The matrices were prepared by either dry granulation(slugging) , or wet granulation method using chloroform as a solvent evaporation vehichle. The cumulative release was adjusted by using polyvinylpyrollidone (PVP) or ethylcellulose (EC) polymers .The results indicated that   both methods of preparation were valid for incorporation PTX as a sustained release granules .Moreover ,the results revealed that best polymer used  was Eudragit RSPM in 3:20 polymer drug ratio .Besides to that ,   the results indicated that the release profiles were affected by  pH- medium&

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Publication Date
Fri Feb 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
A Standard Study of the Role of the Tourism Sector in Achieving Economic Growth in Tunisia for the Period (1995-2017
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This study examines the relationship between the increase in the number of tourists coming to Tunisia and GDP during the period 1995-2017, using the methodology of joint integration, causal testing and error correction model. The research found the time series instability of the logarithm of the number of tourists coming to Tunisia and the output logarithm but after applying the first differences, these chains become stable, THUS these time series are integrated in the first differences. Using the Johansson method, we found the possibility of a simultaneous integration relationship between the logarithm of the number of tourists coming to Tunisia and the logarithm of GDP in Tunisia, and there is a causal relationship in one direc

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Publication Date
Thu Apr 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Using Project Management Maturity Model to Evaluate Construction Sector -Organizations. Case Study at the Department of buildings - Karkh first
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The education sector suffers from many problems, including the scarcity of schools that can absorb the increasing number of students in light of the increasing population growth rate, as some regions suffer from a lack of opening of new schools or the expansion of existing schools to increase their capacity so that attention is required. The research sought to identify the level of maturity of project management at the research site (Building Department in Al-Karkh I/ Ministry of Education) Being responsible for educational projects and their implementation and to know that, the ten areas of the knowledge guide to project management PMBOK have been adopted according to the PM3 model (one of the models of maturity

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