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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
Tue Feb 13 2024
Journal Name
The International Journal Of Oral & Maxillofacial Implants
The Accuracy of Intraoral Registration for Dynamic Surgical Navigation in the Edentulous Maxilla
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Purpose: Despite the high clinical accuracy of dynamic navigation, inherent sources of error exist. The purpose of this study was to improve the accuracy of dynamic navigated surgical procedures in the edentulous maxilla by identifying the optimal configuration of intra-oral points that results in the lowest possible registration error for direct clinical implementation. Materials and methods: Six different 4-area configurations were tested by 3 operators against positive and negative controls (8-areas and 3-areas, respectively) using a skull model. The two dynamic navigation systems (X-Guide® and NaviDent®) and the two registration methods (bone surface tracing and fiducial markers) produced four registration groups. The accuracy of the

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Publication Date
Wed Mar 30 2022
Journal Name
College Of Islamic Sciences
The grammatical approach to explain Bant Souad's poem (Explanation of Ibn Hisham as a model) a . M . Dr. Abdul Hamid Hamad shehatha Mustansiriya University Faculty of Basic Education the department of Arabic language
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This study is concerned with shedding light on the grammatical method of Ibn Hisham Al-Ansari (761 AH), in his explanation of Bant Souad’s poem by the poet Kaab bin Zuhair, and I included a brief description of Ibn Hisham’s life with a number of explanations of this poem, then clarified the most important features of this method The grammar represented by his reliance on hearing and presenting it to analogy with mention of types of analogy, as well as his attribution of opinions to their owners with weighting, selection and balancing, and his attention to reasoning and a number of grammatical ailments, and his approach is also distinguished by following the method of fractal.

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Publication Date
Mon Oct 19 2020
Journal Name
International Journal Of Psychosocial Rehabilitation
The effect of using the interactive video accompanying the static training in learning some basic skills of a model school in squash
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Lately great interests have emerged to find educational alternatives to teach and improve motor skills according to modern educational methods that take into account individual differences and speed in learning for the learner through individual learning that the learner adopts by teaching himself by passing through various educational situations to acquire skills and information in the way he is The learner is the focus of the educational process and among these alternatives the interactive video, the researchers noted through the educational training units at the Model Squash School of the Central Union, and that most of the methods and methods used in learning basic skills take a lot of time in the educational program and do not involve

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Publication Date
Fri Dec 01 2017
Journal Name
Journal Of Economics And Administrative Sciences
A Comparison between Methods of Laplace Estimators and the Robust Huber for Estimate parameters logistic regression model
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The logistic regression model regarded as the important regression Models ,where of the most interesting subjects in recent studies due to taking character more advanced in the process of statistical analysis .                                                

The ordinary estimating methods is failed in dealing with data that consist of the presence of outlier values and hence on the absence of such that have undesirable effect on the result.    &nbs

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Publication Date
Wed May 18 2016
Journal Name
Al-academy
The Role of T.V. Shaws in Transmitting Violence in Children: An Analytic Study for T.V. Chanels for Children During 1/3/2014 – 1/9/2014: يوسف محمد حسين
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Our study comes up to clarify the role of television in spreading the culture of violence with a child. This study represents one of the important studies that have tried to highlight the impact of these programmes, particularly cartoons, on the child's behaviors, actions and acquired habits.Violence considers a common phenomenon among the people, as the role of the media, particularly TV has a vital role due to its properties, characteristics and its significant impact on different segments and groups in society and in children particularly through exposure to programmes of films.The results of the study have been affected by the rising proportion of females to males, and that the contribution of real life has a big role in the child ac

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Publication Date
Mon Oct 02 2023
Journal Name
Journal Of Polymer Research
Morphological study of porous aromatic schiff bases as a highly effective carbon dioxide storages
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Carbon dioxide (CO2) capture and storage is a critical issue for mitigating climate change. Porous aromatic Schiff base complexes have emerged as a promising class of materials for CO2 capture due to their high surface area, porosity, and stability. In this study, we investigate the potential of Schiff base complexes as an effective media for CO2 storage. We review the synthesis and characterization of porous aromatic Schiff bases materials complexes and examine their CO2 sorption properties. We find that Schiff base complexes exhibit high CO2 adsorption capacity and selectivity, making them a promising candidate for use in carbon capture applications. Moreover, we investigate the effect of various parameters such as temperature, and pressu

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Publication Date
Mon Jun 03 2024
Journal Name
Research Journal Of Chemistry And Environment
Molecular study of two medicinal leech species
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he genus Hirudo is an invertebrate animal that got major concerns to human. However, genetics of Hirudo has been unwell considered in Iraq. In order to gain a deeper understanding in the outline of the genetic of Hirudo that were used in alternative medicine clinics, nineteen specimens of Hirudo were obtained. Fourteen of them (H.verbana, n=10; H. orientalis, n=4) were obtained from some different clinics and scientific centres in Baghdad, Iraq between January and March 2022, these specimens were considered as non-local leeches. The other (native isolates) leeches (H. orientalis, n=5) were collected in 2014 from two localities in Erbil, northern Iraq. ITS-2, COI and 12S-rRNA of Hirudo spp were amplified using conventional polymerase chain r

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Publication Date
Wed Aug 01 2018
Journal Name
Association Of Arab Universities Journal Of Engineering Sciences
Slow sand filtration as a tertiary treatment for the secondary effluent from sewage treatment plant
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A field-pilot scale slow sand filter (SSF) was constructed at Al-Rustamiya Sewage Treatment Plant (STP) in Baghdad city to investigate the removal efficiency in terms of Biochemical Oxygen Demand (BOD5), Chemical oxygen demand (COD), Total Suspended Solids (TSS) and Chloride concentrations for achieving better secondary effluent quality from this treatment plant. The SSF was designed at a 0.2 m/h filtration rate with filter area 1 m2 and total filter depth of 2.3 m. A filter sand media 0.35 mm in size and 1 m depth was supported by 0.2 m layer of gravel of size 5 mm. The secondary effluent from Al-Rustamiya STP was used as the influent to the slow sand filter. The results showed that the removal of BOD5, COD, TSS, and Chloride were

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Publication Date
Tue Mar 30 2021
Journal Name
Baghdad Science Journal
Future of Mathematical Modelling: A Review of COVID-19 Infected Cases Using S-I-R Model
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The spread of novel coronavirus disease (COVID-19) has resulted in chaos around the globe. The infected cases are still increasing, with many countries still showing a trend of growing daily cases. To forecast the trend of active cases, a mathematical model, namely the SIR model was used, to visualize the spread of COVID-19. For this article, the forecast of the spread of the virus in Malaysia has been made, assuming that all Malaysian will eventually be susceptible. With no vaccine and antiviral drug currently developed, the visualization of how the peak of infection (namely flattening the curve) can be reduced to minimize the effect of COVID-19 disease. For Malaysians, let’s ensure to follow the rules and obey the SOP to lower the

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Publication Date
Sat Jan 01 2022
Journal Name
International Journal Of Research In Social Sciences & Humanities
Staging Violence in Sarah Kane’s Blasted & Ali Abdulnebi al Ziadi’s Fourth Generation: a Comparative Study
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Violence occurs as a daily human action all over the world; it may cause so many kinds of damage to individuals as well as to society: physical, psychological, or both. Many literary authors of different genres have tried their best to portray violence by showing its negative effects, especially playwrights because they have the chance to show people the dangers of violence through performance on stage to warn them against such negatively affected action. It has been a human action since the beginning of human life on this planet when the first crime happened on earth when Cane killed his brother Abel. In our modern world, people are witnessing daily violent actions as a result of destructive wars that turned the humans into brutal beings.

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