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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
Fri Jun 16 2023
Journal Name
Journal Of Humanities And Social Sciences Researches
The Role and Importance of Electronic Automation in Banking Service Development: A Case Study of the Commercial Bank of Iraq
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Electronic banking services appeared as a result of laying the foundations for the application of electronic automation in the banking field, and despite the clear expansion in its adoption and implementation as an inevitable necessity imposed by international and national developments, its application was not ideal according to the level that was expected to occur after the abandonment of traditional banking services, which produced some risks Which is evident in the absence of a legal system, whether at the level of proving and authoritative electronic banking services such as electronic signature, Or at the level of protecting the confidentiality of these services and ensuring that they are not exp

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Publication Date
Tue Dec 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
The Impact of Envy on Workplace Stress A field Study of Faculty Staff at the Technical College of Management-Baghdad
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The research aims to measure the impact of envy on job stress because the topic of envy represents a negative emotion that exists at all organizational levels, which may cause stress in the work environment.

The Research problem is represented by the lack of perception of most of the faculty staff on the negative effects of envy on their well-being in the Technical College of Management - Baghdad, and what is the impact level of envy on their job stress.

To achieve this, the scale of envy was based on two dimensions (being envied, Envying others), While the job stress scale was based on seven dimensions (workload, conflict role, Family factors, work environment, work relationships

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Publication Date
Sun Jan 13 2019
Journal Name
Iraqi Journal Of Physics
A Study of the effect of adding antimony oxide to the coating surfaces of steel and cast Iron by glass
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The study included adding antimony oxide to mixtures of coating metal surfaces (Enameling), after it was selected ceramic materials used in the coating metal pieces of the type of steel and cast iron in two layers. The first is called a ground coat and the second is a cover coat.
Ceramic materials layer for ground coat have been melted down in
platinum crucible at a temperature of 1200oC to prepare the glass
mixture (Frit). It was coated on metals at a temperature of 780oC for
two minutes, while the second layer was prepared glass mixture
(Frit) at a temperature of 1200oC, but was coated at a temperature of
760oC for two minutes.
Underwent tests crystalline state of powders (Frits) and enameled samples using X-ray di

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Publication Date
Tue Oct 01 2013
Journal Name
Journal Of Economics And Administrative Sciences
The applicability of green productivity tools: An analytical study in a sample of industrial companies in the province of Nineveh
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                The current research aims to identify the most important green productivity tools GPT and the possibility of applied in industrial companies in general and the companies operating in the province of Nineveh, in particular, as well as the study of some personality characteristics and functional, which is believed to be an impact on the application of these tools in industrial companies. Accordingly, the research community of managers in the company of medicines and medical supplies ready-made clothes _ operating in the province of Nineveh, who are (80) while the manager was subjected to research procedures (49) Director representing (61.25%)

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Publication Date
Wed Aug 11 2021
Journal Name
International Journal Of Pharmaceutical Research
Evaluation of Serum Adropin Levels in Nonalcoholic Fatty Liver Disease as A Complication of Hypothyroidism In Iraqi Patients المؤلفون
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Publication Date
Thu Dec 01 2016
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
FIRST RECORD OF NIGRA SCALE, PARASAISSETIA NIGRA (NIETNER, 1861) (HEMIPTERA; COCCIDAE) AS A PEST OF FIG TREES IN IRAQ
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     The nigra scale, Parasaissetia nigra (Nietner, 1861) (Hemiptera, Coccidae) recorded as a new insect pest attacking fig trees, Ficus carica (Moraceae) in Iraq. It was observed during April 2014 in residential garden at Al-Hurriyah district in Baghdad.

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Publication Date
Thu Aug 28 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Assessment of cortisol as salivary psychological stress marker in relation to temporomandibular disorders among a sample of dental students
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Background: University dental students perceived a higher level of stress prior to the final exam associated with raised salivary cortisol levels which could be considered as a useful noninvasive biomarker for measuring acute stress. Using a Helkimo anamnestic and clinical dysfunction scoring for temporomandibular disorders can give a better insight about the association of this marker and temporomandibular joint disorders. The aim of this study was to evaluation level of salivary cortisol in stressor students with temporomandibular disorder and the relation between this marker in relation to temporomandibular disorder severity. This might give a better understanding to the role of psychological stress as an etiological factor for developin

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Publication Date
Mon Jun 01 2020
Journal Name
P J M H S
The influence of Breast Cancer Molecular Subtypes on Metastatic pattern in Iraqi patients
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Publication Date
Thu Mar 01 2007
Journal Name
Al-khwarizmi Engineering Journal
An experimental comparative study between polypropylene and laminated lower limb prosthetic socket
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Most researchers concentrate their studies on the design, stress and pressure distributions of the prosthetic socket. A little attention is considered for the stiffness of the various materials of the prosthetic sockets. Prosthetic laminated sockets in Iraq are costly to be manufactured while polypropylene socket is relatively cheap in comparing with the laminates.

Experimental study is conducted to compare the stiffness of five prosthetic sockets made of different materials. Compression, three point flexural and tensile tests are implemented by the Testometric machine. The laminate sockets give better results in compression than polypropylene. Polypropylene gives good results in bending compared with the laminate sockets. When t

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Publication Date
Wed Jun 06 2001
Journal Name
مجلة العلوم الاقتصادية والادارية
Double cross-over and cross-over with extra period designs -comparative study-
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The goal of the research is to find the optimization in the test of the appropriate cross-over design for the experiment that the researcher is carrying out (under assumption that there are carry-over effects of the treatments) to posterior periods after the application period (which is often assumed to be the first period). The comparison between the double cross-over design and the cross-over design with extra period. The similarities and differences between the two designs were studied by measuring the Relative Efficiency (RE) of the experiment.

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