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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 Jan 01 2023
Journal Name
Brazilian Dental Science
Wound healing effect of a one-week Aloe Vera mouthwash: a pilot study
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Publication Date
Tue Dec 15 2020
Journal Name
Al-academy
Dramatic Construction in Quranic Text Surah Taha – A model: جبار خماط حسن
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There are many varied studies that dealt with the dramatic construction, especially books and studies that addressed drama in its construction and the method of writing it, that no textbook or a general cultural content is void of tackling the dramatic text in its construction and how the dramatic action develops in it. Therefore, a question occurs to the mind about the feasibility of dealing with the dramatic construction in this time, where many contemporary studies of dramatology and its relation and the contemporary critical directions are accumulating. This question many have two realistic aspects, yet the novelty and originality that this research shows lie in addressing a refined linguistic text in its style and connotations, such

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Publication Date
Fri Jun 01 2018
Journal Name
Journal Of The College Of Languages (jcl)
A Pragmatic Study of English Honorific Forms
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         It is axiomatic that languages mirror  the world view of their users. Manipulating honorific forms  among people inevitably reflects this truth . Honorifics are conventionalized forms or expressions  manifested in all the world's languages and  are used to  express the social status of the participants in the verbal interaction and to convey indications like politeness and respect  . English is no exception. However the question is what exactly creates these forms and their meanings. Although  honorifics have been extensively researched from a grammatical and semantic  angle  , yet they haven’t received that significant  attention  i

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Publication Date
Mon Mar 08 2021
Journal Name
Baghdad Science Journal
Solar ray tracing programs to find new types of solar
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Anew Solar concentrator have been designed in this paper, this concentrators Were based on the total internal reflection in a prism, the prism angles has been calculated by depending on the solar incident ray angle in baghdad for a year. The optical design consist ofa triangular presume, Where the solar cells on one side of the prism Wh?le the prism head towered the south. The results show that there is an increasing in the solar ray concentrators and the cell area is reduced.

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Publication Date
Sun Dec 31 2023
Journal Name
International Journal For Humanities & Social Sciences (ijhs)
‘Ambivalence’ as a Concept in John Clare's Middle and Late Poetry
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        This paper signifies the contradictory point of view in John Clare’s poetry. Clare (1794-1864) is an English romantic poetry in the nineteenth century, who writes more than ten volumes about nature. So, this study highlights the concept of Psychoanalytic theory which is ‘ambivalence’ and how through this theory can interpret any literary text on the basis of utilizing psychoanalytic methods to literary texts in order to reveal the author's inner emotions such as motives, dreams, as well as wishes. Consequently, the concept of  ‘ambivalence’ has a lot in common with the human psyche and its struggles. Sometimes the reader finds the author/poet talking about something real or a notion with pleasant sentiments

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Publication Date
Sat Jan 01 2022
Journal Name
International Journal Of Research In Social Sciences & Humanities
COLLABORATIVE WRITING AS A MEANS IN DEVELOPING EFL LEARNERS’ WRITING PERFORMANCE
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Collaborative learning is a way that prepares students practically for real-world applications. Working together as teamwork to execute various writing skills is essential in most professions since it increases the level of experience. Thus, the current study aims to identify the role collaborative writing in developing students' level of performance in writing. It is qualitative in nature since the researcher depended on the extant literature in achieving the objective of the study. The researcher touched upon related theories that addressed Collaborative learning, categories, and problems .It concluded that collaborative writing increases the students’ self-confidence, self-esteem, creativity, and motivation through the interact

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Publication Date
Mon Jul 25 2022
Journal Name
International Journal Of Health Sciences
Ca242 as a potential prognostic marker in colorectal cancer Iraqi patients
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Background: Colorectal cancer is the third most common cancer-related mortality worldwide, and its prevalence is increasing among many nations.  Aim of the study: Investigate the predictive value of carbohydrate antigen 242 (CA242) in comparison to the CEA biomarker and to estimate the significance of CA242 as prognosis maker in colorectal cancer patients. Methods: a case-control study with a total of 150 individuals, 100 patients (59 males, 41 females) and 50 healthy controls (26 males, 24 females). using an enzyme-linked immunosorbent (ELISA) to determine the serum levels of CA242 and CEA. The study was carried out at the gastroenterology consultation clinic of the oncology teaching hospital between November 2020 and February

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Publication Date
Mon Oct 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
measure the relationship between imported inflation and foreign trade in the Iraqi economy for long 1990-2015 using model nardl
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The study aims to discuss the relation between imported inflation and international trade of Iraqi economy for the period (1990-2015) by using annual data. To achieve the study aim, statistical and Econometrics methods are used through NARDL model to explain non-linear relation because it’s a model assigned to measure non-linear relations and as we know most economic relations are non-linear, beside explaining positive and negative effects of imported inflation, and to reach the research aim deductive approach was adopted through using descriptive method to describe and determine phenomenon. Beside the inductive approach by g statistical and standard tools to get the standard model explains the

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Publication Date
Sat Jul 15 2023
Journal Name
2023 6th International Conference On Engineering Technology And Its Applications (iiceta)
Methodology for the Design and Programming Methods for a Smart Home
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Publication Date
Mon Mar 25 2019
Journal Name
Al-academy
Melodic Characteristics of Oud Instrument Compositions with the Iraqi Symphony Orchestra (Saleem Salim) A Model: رعد عدنان علوان
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The variety of ideas and freedom of expression among the authors who are looking for everything new that serves the goals of musical and aesthetic expression, which calls for the use of traditional musical instruments with the great composition of musical instruments known as the orchestra represents a great challenge in several aspects. The incompetence of some of these instruments or limited capabilities or its costly method of performance sometimes forbids its use permanently in this great composition. It was necessary to have some problems facing the composer and the player on the one hand and the recipient on the other hand, who must be looking for perfection. Among those instruments that are used regularly in the works of the orche

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