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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 Feb 12 2026
Journal Name
Journal Of Baghdad College Of Dentistry
An evaluation of three fissure sealants microleakage with presence or absence of bonding agent through time intervals (In vitro study)
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Background: Pit and fissure sealant have been considered an outstanding adjunct to oral health care in the decrease of occlusal caries onset and low progression. The aims of this in vitro study were to evaluate the marginal microleakage of three different types of fissure sealants (SDI, Tg and tetric N-flow) by time interval, one day and 45 days, in the presence or absence of bonding agent among maxillary and mandibular teeth. Materials and methods: Seventy two sound human maxillary and mandibular first premolar teeth were collected which were free from obvious carious lesions. The teeth were randomly divided into two main equal groups, group (1) and group (2), each group consists of (36) teeth involving equal numbers of maxillary and mandi

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Publication Date
Mon Apr 01 2019
Journal Name
Journal Of Educational And Psychological Researches
The Effectiveness of a Teaching Strategy Based on the Cognitive Model of Daniel in the Development of Achievement and the Motivation of learning the School Mathematics among the Third Intermediate Grade Students
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This research aims to examine the effectiveness of a teaching strategy based on the cognitive model of Daniel in the development of achievement and the motivation of learning the school mathematics among the third intermediate grade students in the light of their study of "Systems of Linear Equations”. The research was conducted in the first semester (1439/1440AH), at Saeed Ibn Almosaieb Intermediate School, in Arar, Saudi Arabia. A quasi-experimental design has been used. In addition, a (pre & post) achievement test (20 Questions) and a (pre & post) scale of learning motivation to the school mathematics (25 Items) have been applied on two groups: a control group (31Students), and an experimental group (29 Students). The resear

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Publication Date
Thu Jan 04 2024
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Creative accounting practices for supply contracts and the role of internal audit in reducing them: An exploratory study on a sample of industrial companies in Iraq
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Abstract:

                The internal control is the tool through which it is possible to verify and ensure the implementation of tasks in accordance with the established plans and programs and to evaluate the level of performance that is implemented within the different companies.

A guarantee from the supplier with the absence of a specialized technical committee that follows up the stages of implementing the contract and disbursing all amounts of financial dues to the supplier before completing the implementation of the contract and overlooking the non-implementation of some clauses of the contract by the committee in charge of

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Publication Date
Wed Oct 01 2014
Journal Name
Journal Of Economics And Administrative Sciences
Spatial Regression Model Estimation for the poverty Rates In the districts of Iraq in 2012
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Theresearch took the spatial autoregressive model: SAR and spatial error model: SEM in an attempt to provide a practical evident that proves the importance of spatial analysis, with a particular focus on the importance of using regression models spatial andthat includes all of them spatial dependence, which we can test its presence or not by using Moran test. While ignoring this dependency may lead to the loss of important information about the phenomenon under research is reflected in the end on the strength of the statistical estimation power, as these models are the link between the usual regression models with time-series models. Spatial analysis had

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Publication Date
Sun Dec 01 2019
Journal Name
Saudi Medical Journal
The diagnostic power of circulating micro ribonucleic acid 34a in combination with cancer antigen 15-3 as a potential biomarker of breast cancer
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Publication Date
Mon Mar 01 2021
Journal Name
Journal Of Dental Sciences
Evaluation of the efficacy of lycopene gel compared with minocycline hydrochloride microspheres as an adjunct to nonsurgical periodontal treatment: A randomised clinical trial
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Crossref (15)
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Publication Date
Mon Mar 01 2021
Journal Name
Journal Of Dental Sciences
Evaluation of the efficacy of lycopene gel compared with minocycline hydrochloride microspheres as an adjunct to nonsurgical periodontal treatment: A randomised clinical trial
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Publication Date
Wed Nov 07 2018
Journal Name
Iraqi National Journal Of Nursing Specialties
Knowledge of Breastfeeding: A descriptive study among mothers in Kirkuk Governorate
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Aims: The present study aims at assessing mothers’ knowledge of breastfeeding in Kirkuk governorate,
besides determining the relationship between mothers’ knowledge and some of their demographic
attributes.
Methodolgy: A descriptive study was used the assessment approach and applied on mothers in Kirkuk
governorate from January 15th 2011 to July 25th
, 2011. Non-probability sampling a convenience sample of
(72) mothers, attending pediatric general hospital in Kirkuk governorate for following up the health status
of their children, was selected for the purpose of the study. A questionnaire was developed for the
purpose of the study. It was comprised of two parts; the first part includes the mothers' demographic

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Publication Date
Mon Nov 01 2021
Journal Name
Journal Of Language And Linguistic Studies
A Pragma-Linguistic Study of Suggestive Ambiguity in Selected Political Texts.
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Suggestive ambiguity is a strategy of defense and maneuvering as it provides the speaker both protection and function. To put it differently, it helps the speaker to say whatever he likes and at the same time gives his opponents and friends the interpretation they desire. This is possible due to the flexibility of the linguistic expressions that the speaker uses. To be more clear, the context of situation, peoples' background and world knowledge interact with the significance of the linguistic expressions reaching an allusive situation where two interpretations, positive and negative, are available to the addressees. Such situation enables the addressers to implicate different ideas or messages, accusations, inciting violence, etc. The pres

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Publication Date
Fri Jun 29 2018
Journal Name
Journal Of The 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:

  1. Is it possible to examine praise poetry as a tagmeme?
  2. 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.

   &nbs

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