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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 Oct 01 2014
Journal Name
Al–bahith Al–a'alami
The electronic news bulletin of the ministry of higher education and scientific research: A study in the newspapers of: (AL-Taakhi, AL-Zaman, ALAdala,AL-Sabah and Baghdad) for period from 2nd October 2011 to 1st November 2011
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The research aims to know the reverberation of the the electronica news bulletin of the ministry of higher education and scientific research  in the newspapers of: (AL-Taakhi, AL-Zaman, ALAdala,AL-Sabah and Baghdad) for period from 2nd October 2011 to 1st November 2011 to explain its activity and advantage for the other newspapers and to show the importance which the newspapers showed for the study of the news subject in the bulletin, as well as,to show the proportional differences in which the newspapers interested in the subjects of the published news, and to reach to the results which lead us to good conclusions for the service of decision owner and open new horizons for the researchers to expanding in the s

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Publication Date
Tue Mar 03 2026
Journal Name
Al–bahith Al–a'alami
THE ISSUES OF YOUTH IN THE TALK SHOWS IN THE IRAQI SATELLITE CHANNELS:: (An Analytical Study of the Shabab wa Banat Program at Al-Sumaria TV Channel and of the Hala Shabab at Al-Iraqia TV Channel) (A Research Drawn from a Master’s Thesis)
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The purpose of this research is to identify the youth issues in Talk Shows in the Iraqi satellite channels via monitoring a sample of episodes of the Talk Shows  episodes which are concerned and analyzed the youth issues in the Iraqi satellite channels, namely, «Hala Shabab Program» at Al-Iraqia satellite Channel and «Shabab wa Banat Program» at Al-Sumaria satellite Channel by recording and re-watching them again. This research is classified as one of descriptive researches. The survey method was adopted in this study.

For this purpose, the researcher prepared an analysis form. The researcher de

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Publication Date
Thu Nov 01 2007
Journal Name
University Of Baghdad
The Psychic Experience and its Effects on the Creative Process: A Study in Selected Poems By Allen Ginsberg and David Gascoyne
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Evidences indicate that human beings were preoccupied with extreme forms of mental and psychic experiences long before they were recorded in literature. Greek myths and legends appear to include symbolizations of delusions, mania, and other bizarre forms of thought and behaviuor. The figure of the mad man or woman is analogous to the wild man, or the imaginary being who appears in various forms throughout western literature and art. Various studies refer to the notion of the wild man as a response to a persistent psychological urge. This urge gives an external expression and a valid form to the impulses of reckless physical self-assertion which is believed to be hidden in all of us, but is normally kept under control. Such impulses were exp

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Publication Date
Sun Dec 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
The Role of SMEs & The Justifications For Its incubation : Survy Study
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Abstract

We can see the phenomena of small and medium-sized enterprises, by important and a new subject contemporary, thro related between important concept that develop and add. This research focused on the important concept of small and medium-sized enterprises, in public and privet sectors. small and medium-sized enterprises discrimination by large filer ratio in the especially at the first years when they started because of the limited managerial skills, financial recourses and marketing problems. On it they will creative new procedures. this research treatment the core issues about wakens local and international enterprises, so threat. the goals of this research are extended malty dimension concept o

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Publication Date
Wed Oct 11 2023
Journal Name
Journal Of Educational And Psychological Researches
Motivations of Volunteers in Jordan: An Exploratory Study Based on a Sample of University Students within the Context of their Social Relations
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Volunteerism is an element included in many human cultures. It represents a positive cooperative act between individuals and groups. It expresses the social value systems. As a social phenomenon, it develops in societies according to innumerous circumstances and conditions. This study uses a functional approach that assumes that volunteering performs six functions for volunteers. Namely, we assume that volunteering (1) creates a sense of protection (2) meets significant cultural values (3) improves professional status of volunteers, (4) strengthens their social relationships, (5) helps them achieve a better understanding of life, and finally, (6) enhances their outlook and self-esteem. The central aim of the study is to discuss these fun

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Publication Date
Tue Jun 01 2021
Journal Name
Baghdad Science Journal
The Existence of a Polynomial Inverse Integrating Factors and Studies About the Limit Cycles for Cubic, Quartic and Quintic Polynomial Systems
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Publication Date
Wed Jan 02 2019
Journal Name
Journal Of Educational And Psychological Researches
A training program for chemistry teachers based on the knowledge economy and its impact on the productive thinking of their students
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       The current research aims to build a training program for chemistry teachers based on the knowledge economy and its impact on the productive thinking of their students. To achieve the objectives of the research, the following hypothesis was formulated:

   There is no statistically significant difference at (0.05) level of significance between the average grades of the students participating in the training program according to the knowledge economy and the average grades of the students who did not participate in the training program in the test of productive thinking. The study sample consisted of (288) second intermediate grade students divided into (152) for the control group

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Publication Date
Tue Aug 15 2023
Journal Name
Bionatura
The role of ferric citrate in a sample of Iraqi patients on hemodialysis- A randomized controlled clinical trial
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Background: Uncontrolled hyperphosphatemia is the main difficulty facing staff treating patients with end-stage renal disease on hemodialysis. Sevelamer and calcium-containing phosphate binders have been associated with cost burden and tissue calcification, respectively. Therefore, the current trial was targeted to investigate the efficacy of a new phosphate binder, ferric citrate, in a sample of Iraqi patients with end-stage renal disease on hemodialysis. Keywords: Ferric citrate, Hemodialysis Phosphate binder

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Publication Date
Sat Mar 30 2024
Journal Name
Al-qadisiyah Journal For Engineering Sciences
Investigation of an automobile air-conditioner with a liquid-suction heat exchanger using R134a and R1234yf
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Air-conditioning systems (ACs) are essential in hot and humid climates to ensure acceptable ambient air quality as well as thermal comfort for buildings users. It is essential to improve refrigeration system performance without increasing the effects of global warming potential (GWP) and ozone depletion potential (ODP). The main objective of this study is to evaluate the performance of an air conditioning system that operates with a liquid suction heat exchanger (LSHX) through implementing refrigerants with zero OPD and low GWP (i.e., R134a and R1234yf). Liquid suction heat exchanger (LSHX) was added to an automobile air conditioning system (AACS).When Liquid suction heat exchanger was added to the cycle, primary results indicated t

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Publication Date
Sat Jan 25 2020
Journal Name
Indian Journal Of Forensic Medicine & Toxicology
A Stereomicroscopic Analysis of Dentinal Micro Cracks after Root Canal Preparation Using Four Different Rotary Instruments.
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A variety of single-engine driven files and inematics have been introduced to improve the clinical performance of NiTi rotary files. The purpose of this in vitro study was to measure and compare the incidence of dentinal defects after root canal preparation with different single file systems.

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