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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
Thu Dec 01 2016
Journal Name
Journal Of Engineering
A Laboratory Study Attempt of Flow and Energy Dissipation in Stepped Spillways
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A new laboratory study conducted on stepped spillways in order to investigate their efficiency of dissipating flow energy. All previous study on stepped spillway indicated that the flow energy dissipation decreased as increasing in discharge. Increasing in the step numbers and the spillway slope led to energy dissipation decrease. In this study, an experimental attempt to increase energy dissipation at variable discharges was performed on stepped spillway and that leads to decreasing the cost of initiating the stilling basin or may be ignoring it. Five spillways were constructed from concrete and tested to investigate and compare among them. Three were roughed by gravel with different size for each one, one of them was s

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Publication Date
Thu Jun 09 2022
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Safety Profile of Biological Drugs in Clinical Practice: A Retrospective Pharmacovigilance Study
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Biological drugs have an active substance that is made by a living organism or derived from a living organism. They are one of the important therapy options used in a wide range of diseases especially life-threatening diseases. Biological therapy opens new opportunities for treating different diseases for which drug therapy is minimal, but they have considerable differences in the safety consequences in comparison with non-biological drugs. The aim of the current study was to assess the post-marketing safety profile of biological drugs used in Iraqi hospitals by the analysis of the reported adverse drug reactions regarding their severity, seriousness, preventability, expectedness, and outcome. It is a retrospective study of the individu

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Publication Date
Fri Oct 20 2023
Journal Name
Al-ameed Journal For Medical Research And Health Sciences
Perceptions of Nursing Students about COVID-19 Transmission: A Multi University Study
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Publication Date
Sun Feb 20 2022
Journal Name
Papers In Physics
Electronic and optical properties of nickel-doped ceria: A computational modelling study
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Cerium oxide CeO2, or ceria, has gained increasing interest owing to its excellent catalytic applications. Under the framework of density functional theory (DFT), this contribution demonstrates the effect that introducing the element nickel (Ni) into the ceria lattice has on its electronic, structural, and optical characteristics. Electronic density of states (DOSs) analysis shows that Ni integration leads to a shrinkage of Ce 4f states and improvement of Ni 3d states in the bottom of the conduction band. Furthermore, the calculated optical absorption spectra of an Ni-doped CeO2 system shifts towards longer visible light and infrared regions. Results indicate that Ni-doping a CeO2 system would result in a decrease of the band gap. Finally,

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Publication Date
Mon May 25 2020
Journal Name
Journal Of Xi'an University Of Architecture & Technology
Iraqi Virtual Science Library (IVSL)): A field study of Iraqi researcher’s viewpoint
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The aim of the research is to shed light on the stages of developing the Iraqi virtual science Library(IVSL) project, and to define its distinctive role in providing all kinds of electronic resources to researchers from professors and graduate students, to identify its contents , the entry interfaces and applications of use, and provide them through electronic portals to publishing houses, research institutions and international universities, The research sample included the teaching staff and researchers participating in educational qualification courses at the Continuing Education Center at the University of Baghdad, The research population and its sample consisted of the category of (IVSL) users, and its sample (387) users. Analysis meth

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Publication Date
Thu Mar 24 2022
Journal Name
Arab World English Journal
Collocation Networks of Selected Words in Academic Writing: A Corpus-Based Study
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This study aims at shedding light on the linguistic significance of collocation networks in the academic writing context. Following Firth’s principle “You shall know a word by the company it keeps.” The study intends to examine three selected nodes (i.e. research, study, and paper) shared collocations in an academic context. This is achieved by using the corpus linguistic tool; GraphColl in #LancsBox software version 5 which was announced in June 2020 in analyzing selected nodes. The study focuses on academic writing of two corpora which were designed and collected especially to serve the purpose of the study. The corpora consist of a collection of abstracts extracted from two different academic journals that publish for writ

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Publication Date
Mon Feb 28 2022
Journal Name
Journal Of Educational And Psychological Researches
Classroom Teachers’ Perceptions of Response to Intervention Implementation: a Qualitative Interview Study
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The purpose of this interview study was to explore teachers’ perceptions of Response to Intervention (RtI) implementation in their school. Particularly, the study explored teachers’ knowledge of RtI, teachers’ perceptions of RtI their intervention/instruction in school, and teachers’ suggestions of RtI implementation in their school. The study design was a qualitative interview in nature and data were collected from face-to-face interviews with four teachers in one school. The findings revealed that RtI means to identify students’ problems; the positive teachers’ perceptions of their implementation included: (a) students who demonstrate progress through RtI are those who receive private education services, (b) progress monito

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Publication Date
Thu Jun 30 2022
Journal Name
Journal Of Current Researches On Educational Studies
Study of Swear Words in Selected Literary Works: A Syntactic-Semantic Analysis
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BN RASHİD, 2022

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Publication Date
Wed Dec 11 2019
Journal Name
Journal Of The College Of Education For Women
Differences of Style between English and Arabic Political Discourse: A Contrastive Study
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Traditionally, style is defined as the expressive, emotive or aesthetic emphasis added linguistically to the discourse with its meaning is the same. In the current study, however, style is defined as the linguistic choice that the language users can make for specific purposes.

    This study, thus, aims at analyzing political Arabic and English speeches to find out whether there are differences of style between English and Arabic and whether the choices the language users make  can show any traits of their psychological status.

    To fulfill the above aims, the study hypothesizes that English and Arabic  speeches can be analyzed stylistically and that there are stylistic difference

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Publication Date
Fri Sep 15 2017
Journal Name
كلية الاداب جامعة بغداد
A Contrastive study of ‘Inversion ‘ in Modern English and Modern Arabic Poetry
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The present paper respects 'inversion' as a habit of arranging the language of modern English and Arabic poetry . Inversion is a significant phenomenon generally in modern literature and particularly in poetry that it treats poetic text as it is a violator to the ordinary text. The paper displays the common patterns and functions of inversion which are spotted in modern English and Arabic poetry in order to show aspects of similarities and differences in both languages. It concludes that inversion is most commonly used in English and Arabic poetry in which it may both satisfy the demands of sound correspondence and emphasis. English and Arabic poetic languages vary in extant to their manipulation of inverted styles as they show changeable f

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