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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 Dec 01 2010
Journal Name
Iraqi Journal Of Physics
An Improved Method for the Determination of Airplane Radial Velocity Using Doppler Shift
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In this research velocity of moving airplane from its recorded digital sound is introduced. The data of sound file is sliced into several frames using overlapping partitions. Then the array of each frame is transformed from time domain to frequency domain using Fourier Transform (FT). To determine the characteristic frequency of the sound, a moving window mechanics is used, the size of that window is made linearly proportional with the value of the tracked frequency. This proportionality is due to the existing linear relationship between the frequency and its Doppler shift. An algorithm was introduced to select the characteristic frequencies, this algorithm allocates the frequencies which satisfy the Doppler relation, beside that the tra

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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Study the Quality of Nasopharyngeal plans Using Evaluation Indexes of IMRT and VMAT Treatment planning Techniques
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Radiation treatment has long been the conventional approach for treating nasopharyngeal cancer (NPC) tumors due to its anatomic features, biological characteristics, and radiosensitivity. The most common treatment for nasopharyngeal carcinoma is radiotherapy. This study aimed to assess the better quality of radiotherapy treatment techniques using intensity-modulated radiotherapy (IMRT) and volumetric-modulated arc therapy (VMAT). The VMAT and IMRT are comparative techniques. Forty patients with nasopharyngeal carcinoma and forwarded for radiotherapy were treated with both advanced techniques, IMRT and VMAT, using eclipse software from Varian. The x-ray energy was set at 6 MV. The total prescribed dose was 70 Gy. The results show that the

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Publication Date
Thu Feb 07 2019
Journal Name
Journal Of The College Of Education For Women
Nominal Ellipsis in English & Arabic and its Influence on the Translation of the Meanings of Some Selected Qurànic Verses ( A Contrastive study ): هدى فالح حسن & جمانة شكيب محمد
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Nominal ellipsis is a linguistic phenomenon found in English and Arabic .It is
based on leaving out a part of a nominal construction or more for the sake of good
style , compactness and connectedness .This phenomenon is found in the language of
the Glorious Qur’an .The study in hand is concerned with how translators handle
translating Qur’anic verses which contain ellipted nouns , i ,e. , to what extent the
translated Qur’anic verses are close to the original ones , and to what extent their
translations serve understanding the meanings of the glorious verses while at the
same time maintaining their beauty in style. The study aims at shedding light on
nominal ellipsis in English and Arabic .The study undertak

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Publication Date
Sat Mar 14 2026
Journal Name
Tikrit Journal Of Administrative And Economic sciences
Determination of competency levels and auditor evaluation procedures to the international standard (ISO19011: 2018) A case study at the Ministry of Construction, Housing and General Municipalities/Audit Directorate
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The current research seeks to achieve several objectives, including knowing the extent of the audit directorate of the Ministry of Construction, Housing and General Municipalities of the International Standard (ISO19011:2018) regarding determining the efficiency and evaluation of auditors and diagnosing the gap between requirements and application and knowing the reasons for not applying some of the items in the standard, starting from the problem, The field raised the following question (Does the audit directorate determine the efficiency and evaluation of auditors according to the standard ISO19011:2018?), and the importance of research lies in determining the return that can be achieved by the directorate through its application of stand

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Publication Date
Sat Jan 02 2021
Journal Name
Journal Of The College Of Languages (jcl)
Determining situational dimensions as a method of Equivalence in the source and target language in the translation of Russian and Arab: ( Понимание реальности ) средство полной эквивалентности текста оргинала и текста перевода на русском и арабском языках
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The present paper stresses the direct effect of the situational dimension termed as “reality” on the authors’ thoughts and attitudes. Every text is placed within a particular situation which has to be correctly identified by the translator as the first and the most important step for a good translation. Hence, the content of any word production reflects some part of reality. Comprehending any text includes comprehending the reality’s different dimensions as reflected in the text and, thus illuminating the connection of reality features.

Аннотация 

Исследование под названием  ((«Понимание реальности» средство полно

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Publication Date
Fri Apr 15 2022
Journal Name
Alustath Journal For Human And Social Sciences
The Intersectionality in I’ve Been Meaning To Tell You: A Letter to My Daughter: A Post-Colonial Perspective
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Intersectionality is a concept that focuses on social inequality towards black people and provides an analytical instruments for creating social justice issues in such a way in order to depict how social marginalization, or privilege occurs differently in various social positions. It does this by focusing on the interaction of multiple systems of oppression. Intersectionality is used to examines how the social factors; race, gender, and class can affect the people’s life especially the immigrants, black people, and refuges. This article will depicts how blacks in Canada are segregated and distinguished from white race. David Chariandy’s I’ve Been Meaning To Tell You: A Letter to My Daughter 2018 is analyzed through Kimberle Crenshaw

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Publication Date
Fri Apr 15 2022
Journal Name
Alustath Journal For Human And Social Sciences
The Intersectionality in I've Been Meaning to Tell You: A Letter to My Daughter: A Post-Colonial Perspective
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Intersectionality is a concept that focuses on social inequality towards black people and provides an analytical instruments for creating social justice issues in such a way in order to depict how social marginalization, or privilege occurs differently in various social positions. It does this by focusing on the interaction of multiple systems of oppression. Intersectionality is used to examines how the social factors; race, gender, and class can affect the people’s life especially the immigrants, black people, and refuges. This article will depicts how blacks in Canada are segregated and distinguished from white race. David Chariandy’s I’ve Been Meaning To Tell You: A Letter to My Daughter 2018 is analyzed through Kimberle Crenshaw

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Publication Date
Mon Sep 30 2019
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Synthesized 2nd Generation Zeolite as an Acid-Catalyst for Esterification Reaction
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MCM-48 zeolites have unique properties from the surfaces and structure point of view as it’s shown in the results ,and unique and very sensitive to be prepared, have been experimentally prepared and utilized as a second-generation/ acid - catalyst for esterification reactions of oleic acid as a model oil for a free fatty acid source with Ethanol. The characterization of the catalyst used in the reaction has been identified by various methods indicating the prepared MCM-48 is highly matching the profile of common commercial MCM-48 zeolite. The XRF results show domination of SiO2 on the chemical structure with 99.1% and  agreeable with the expected from MCM-48 for it's of silica-based, and the SEM results show the cubic c

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Publication Date
Sun Jun 30 2019
Journal Name
Journal Of The College Of Education For Women
(Evaluation and Mobility) As Two self-Organizing Posts for University Students
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One of the important goals in the learning process is to be effective learning through the self-direction of the learner , because it has an impact on the effort of learners , it is better to be a learner responsible for learning and independent of the acquisition of knowledge ,

اذ اكدتكثيرAs many have confirmed منFrom الدراساتStudies والادبياتAnd literature انthat فشلالكثير The failure of many منFrom الطلبةStudents فيin a تنظيمgroup المعلوماتthe information ومعالجتهاAnd processed اثناءduring عمليةProcess تعلمهمLearn them لاNo يرجعReturns الىto me انخفاضdrop فيin a درجةDegree ذكائهمTheir intelligence اوor عدمNo

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Publication Date
Sun Dec 01 2013
Journal Name
Baghdad Science Journal
Food dyes as an alternative tracking dye for DNA gel electrophoresis
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The chemical, physical and toxicological effects on health of synthetic dyes that used as tracking dye in the electrophoresis requires seriously search about alternative tracking dye. The present study is aimed to find an alternative dye from safe food dyes which commonly used in food coloring. Five dyes were selected depending on their chemical properties and the availability in local market: Brilliant Blue FCF, Tartrazine, Sunset Yellow FCF, Carmoisine, and green traditional, three dyes were chosen to be mixed as loading buffer: Brilliant Blue FCF, Sunset Yellow FCF as a basic because it give the whole range size of most traditional loading buffers that available in market, and adding the Carmoisine as a new indicator for the bands less t

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