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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
Sat Nov 01 2014
Journal Name
Glob Dermatol
Podophyllin 25% as alternative effective topical therapy for keratoacanthoma
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KE Sharquie, AA Noaimi, Glob Dermatol, 2014 - Cited by 6

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Publication Date
Mon Nov 24 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Early and delayed effect of 2% chlorhexidine on the shear bond strength of composite restorative material to dentin using a total etch adhesive
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Background: Lack of durability of the bond of the dental adhesive systems to tooth structure is one of the most important problems in tooth colored restorative work. This in vitro study was performed to evaluate the effect of 2% chlorhexidine gluconate(CHX) on dentin bond strength by using total etch adhesive system at twenty-four hours and three months of water storage. Material and methods:A flat dentin surface was prepared for forty sound human maxillary premolar teeth which were acid etched with 36% phosphoric acid gel after being divided randomly into four groups of ten teeth each according to storage time and CHX application, theCHX was applied for 60 seconds before adhesive application for groups I and III which were tested after twe

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Publication Date
Thu Aug 01 2019
Journal Name
Journal Of Economics And Administrative Sciences
The Effect of Viral Marketing Technologies on Consumer Behavior _ A survey of a sample of students from the college of administration and economics
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Abstract:

Viral marketing has become one of the modern strategies adopted by organizations in the marketing of products and services. The idea of viral marketing focuses on the social relations between individuals and groups. As a result of the technological development, most organizations have resorted to using the Internet and its applications and social media to market and promote their products. To reach the largest number of consumers to display their products and services in many ways, including text, audio, visual or video and thus affect the behavior of the consumer.

The problem of the study was the following question (do viral marketing technologies have an impact on consumer behavior?)

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Publication Date
Wed Mar 23 2022
Journal Name
Journal Of Educational And Psychological Researches
The Effectiveness of a strategy (fahs) in the development of grammar skills of a sample of secondary school Female Students in Saudi Arabia
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The aim of the present research is to measure the degree of strategic effectiveness (fahs) in the development of grammar skills of high school students in the Kingdom of Saudi Arabia and to achieve the goal of the researcher the researcher used the semi-experimental approach; On ten arbitrators specializing in grammar, morphology, curricula and methods of teaching the Arabic language. After confirming the validity of the guideline, the researcher prepared an achievement test consisting of (22) paragraphs of the type of short answer and multiple choice. The researcher trained a teacher to apply the strategy to the experimental research sample using the (screening) component of (30) students, and the same parameter taught the control sampl

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Publication Date
Fri Jun 01 2018
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
The role of external audit in banking risk management: A typical framework for control testing and banking risk assessment
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Banks face many of the various risks: which are of dangerous phenomena that cause the state achieved a waste of money and a threat to future development plans to be applied to reach the goals set by: prompting banks and departments to find appropriate solutions and fast: and it was within these solutions rely on Banking risk management and effective role in defining and identifying: measuring and monitoring risk and trying to control and take risks is expected to occur in order to encircle and make it in within acceptable limits: and try to avoid them in the future to reduce the losses that are likely to be exposed to the bank: and it began to emerge and dominate a lot of legislation that seeks to structure the year risk management and t

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Publication Date
Wed Aug 05 2020
Journal Name
Open Access Macedonian Journal Of Medical Sciences
The use of Cinnamon (Cinnamomum Bark) for Patients with Chronic Prostatitis/Chronic Pelvic Pain Syndrome: A Randomized Controlled Trial
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BACKGROUND: Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is common, yet no curative treatment identified. Cinnamon is a herbal substance, which has many applications in medicine. AIM: The aim of the study was to study the effect of cinnamon on patients with chronic pelvic pain syndrome. METHODS: Sixty patients with documented CP/CPPS randomized into two groups during 2018 and 2019 in Baghdad. The first group received 60 capsules each contained 1 g of cinnamon. The other group received 60 capsules each contained 1 g of sugar powder (placebo). All the patients instructed to take one capsule twice daily for 1 month. National Institutes of Health-Chronic Prostatitis Symptom Index (NIH-CPSI) was reported for bot

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Publication Date
Thu Jan 27 2022
Journal Name
Nanomaterials
Improving the Melting Duration of a PV/PCM System Integrated with Different Metal Foam Configurations for Thermal Energy Management
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The melting duration in the photovoltaic/phase-change material (PV/PCM) system is a crucial parameter for thermal energy management such that its improvement can realize better energy management in respect to thermal storage capabilities, thermal conditions, and the lifespan of PV modules. An innovative and efficient technique for improving the melting duration is the inclusion of an exterior metal foam layer in the PV/PCM system. For detailed investigations of utilizing different metal foam configurations in terms of their convective heat transfer coefficients, the present paper proposes a newly developed mathematical model for the PV/PCM–metal foam assembly that can readily be implemented with a wide range of operating condition

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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Accounting And Financial Studies ( Jafs )
Use ofBang marking in the management of the cost of food and beverages in the hotel: sector (Case study in a sample of hotels in Baghdad governorate)
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The competition in the hotel sector, globalization and the development of new information have forced the sector to continuously seek new techniques and arrangements to remain competitive through hotel industry companies, including Benchmarking and the application of this method in the hotel sector. The selection of the Rashid International Hotel by the Ministry of Tourism as a leading hotel or benchmark for comparison of other hotels in Iraq, and the selection of two hotels in Baghdad for comparison, namely (Ishtar International Hotel, Baghdad International Hotel) and the choice also by the Ministry of Tourism, N is to correct the course of practice to manage the cost and diagnosis of the weakness of the strengths and weaknesses in the

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Publication Date
Fri Mar 04 2022
Journal Name
Environmental Science And Pollution Research
Geographically weighted regression model for physical, social, and economic factors affecting the COVID-19 pandemic spreading
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Abstract<p>This study aims to analyze the spatial distribution of the epidemic spread and the role of the physical, social, and economic characteristics in this spreading. A geographically weighted regression (GWR) model was built within a GIS environment using infection data monitored by the Iraqi Ministry of Health records for 10 months from March to December 2020. The factors adopted in this model are the size of urban interaction areas and human gatherings, movement level and accessibility, and the volume of public services and facilities that attract people. The results show that it would be possible to deal with each administrative unit in proportion to its circumstances in light of the factors that appe</p> ... Show More
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Publication Date
Fri Feb 01 2019
Journal Name
Indian Journal Of Natural Sciences
Surface Photometry and Morphology Properties of Spiral Galaxies: NGC4725, NGC4639 as Case Study
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In this study, two active galaxies (NGC4725, NGC4639) have been chosen to study their morphological and photometric properties, by using the IRAF ISOPHOTE ELLIPS task with griz-filters. Observations are obtained from the Sloan Digital Sky Survey (SDSS) which reaches now to the DATA Release (DR14). The data reduction of all images (bias and flat field) has been done by SDSS Pipeline. The surface photometric investigation was performed like the magnitude. Together with isophotal contour maps, surface brightness profiles and a bulge/disk decomposition of the images of the galaxies, although the disk position angle, ellipticity, and inclination of the galaxies have been done. Also, the color of galaxies was studied, where chromatic distribution

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