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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 Jan 30 2019
Journal Name
Journal Of The College Of Education For Women
Forced displacement in Iraq its causes and its effects on displaced families (A field study of displaced families to the city of Baghdad)
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After a temporary halt to forced thghebr in different cities of Iraq this methodlogy
opeations returned directiy in the areas of political conflict on the ground which are translated
operations and forced displacement violence es they operations aimed at completing the
forced displacement that occurred after the occupation in(2003)which took an upward curve
publicly after these events and some of which are aimed at the liquidation of some provinces
than any demographic diversity of religious or sectarian or alhens and others aimed at
redemographic distribution within the province itself to produce a net sectarian zones as is the
case in Diyala Nineveh and Babylon Baghdad has the epicenter of sectarian violence and th

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Publication Date
Sun Apr 30 2023
Journal Name
Al-kindy College Medical Journal
Influence of Vitamin D Deficiency on the Level of Salivary cathelicidin LL-37 in relation to Dental Caries Experience: A Case-Control Study
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Background: Vitamin D improves innate immunity by enhancing the expression of antimicrobial peptides. The antimicrobial action of cathelicidin is widespread and effective against cariogenic bacteria. This research aimed to investigate the effect of vitamin D deficiency on the level of salivary cathelicidin concerning dental caries experience.

Subjects and Methods: A case-control study was carried out, and the sample was composed of 80 females; the study group involved 40 females with a serum vitamin D concentration of less than 10 ng/ml. In addition to the control group involving 40 females wh

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Publication Date
Mon Aug 01 2016
Journal Name
Journal Of Economics And Administrative Sciences
Evaluating the level of organizational commitment and its relationship to discipline doctors: an analytical study of the opinions of a sample of doctors in Teaching Remade Hospital
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The aims of this reserch is identify  evaluate the organizational commitment level of (emotional, standard, continuous) and the level of discipline dimensions (functional duties, professional responsibility and ethics) for medical doctors in Ramadi Teaching Hospital due to their relationship with the organization effectiveness the level of completion work and the importance of the expected results in the field respondent

sample of (50) doctors has from all branches and specialties, including specialist doctors consultants and practitioners as well as branches of residence and senior the most prominent results reached are the emotional and the  st

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Publication Date
Sat Oct 01 2022
Journal Name
Al–bahith Al–a'alami
MEDIA AND CUSTOMERS: (An analytical study of the opinions and attitudes of a sample of industrialists in the role of media in directing consumers to national industries)
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The talk about the relationship between the media and industrialists can be the core of a bigger and deeper subject which is the role of these means in increasing sales : First, increasing the customer’s awareness of the importance of goods and the result of the promotion of products. Secondly, increasing investments which do require continuous studies and deep research in order to understand the constantly changing market conditions, and the public’s taste. In this research, we try to find out how industrialists see the role of media in the promotion of products in Iraq today, and how it develops in the future.

There was a reluctance of the industrialists to advertise in the local media, also industrialists see the role of t

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Publication Date
Wed Oct 01 2014
Journal Name
Al–bahith Al–a'alami
TV and educating university youth about the challenges of cultural identity in Iraq Field study of a sample of students at University of Baghdad
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The TV plays an active role in building the general culture of the recipients, which calls for emphasizing its contemporary mission in rebuilding the values that support the development and modernization of diverse societies. Such importance is necessary to explore the challenges facing the cultural invasion, The space opening, which had its cultural returns to the societies, produced a space for alternative values and antagonisms in the cultures and traditions of these societies in the midst of a psychological / social conflict behind a clash with the peculiarities of Muslim societies. Cultural Adtha.
From these points of view, and because the universities are an important stage to announce the demands of the advocates of change and

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Publication Date
Tue Aug 24 2021
Journal Name
Periodicals Of Engineering And Natural Sciences (pen)
A plan for transportation and distribution the products based on multi-objective travelling salesman problem in fuzzy environmental
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Transportation and distribution are the most important elements in the work system for any company, which are of great importance in the success of the chain work. Al-Rabee factory is one of the largest ice cream factories in Iraq and it is considered one of the most productive and diversified factories with products where its products cover most areas of the capital Baghdad, however, it lacks a distribution system based on scientific and mathematical methods to work in the transportation and distribution processes, moreover, these processes need a set of important data that cannot in any way be separated from the reality of fuzziness industrial environment in Iraq, which led to use the fuzzy sets theory to reduce the levels of uncertainty.

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Publication Date
Sun Jun 20 2021
Journal Name
Baghdad Science Journal
Studying the Changes in Solar Radiation and Their Influence on Temperature Trend in Iraq for a Whole Century
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Most studies indicated that the values ​​of atmospheric variables have changed from their general rates due to pollution or global warming etc. Hence, the research indicates the changes of direct solar radiation values ​​over a whole century i.e. from 1900 to 2000 depending on registered data for four cities, namely (Mosul - Baghdad - Rutba - Basra. Moreover, attemptsto correlate the direct solar radiation with the temperature values have been ​​recorded over that period. The results showed that there is a decreasing pattern of radiation quantities over time throughout the study period, where the value of direct radiation over the city of Baghdad 5550 w/m2 was recorded in the year 1900, but this ratio decreased cle

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Publication Date
Fri Oct 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
The reflection of strategic knowledge management on an improvement of excellent performance: A survey study at the Institution of Industrial Development and Research- the Ministry of Iraqi Industry (IDRMII)
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The current study aims to investigate the effect of strategic knowledge management practices on an excellent performance at the Institution of Industrial Development and Research- the Ministry of Iraqi Industry (IDRMII). The present research is designed according to the descriptive method. To achieve the mentioned research objective, the researchers used the questionnaire as the main data collection tool. The research sample was 150 managers who are working at the top and middle management levels. To analyses the data gathered and reaching the results, several statistical techniques were used within AMOS.V25, SPSS.V21Software, This study reached a set of results, the most important of which is the existence of a positive correlat

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Publication Date
Thu Jun 15 2017
Journal Name
Journal Of Baghdad College Of Dentistry
The effect of nano-hydroxy apatite on re-mineralize white spot lesions prior to orthodontic adhesive removal by different techniques (An In vitro comparative study)
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Background: White-spot lesion is one of the problems associated with the fixed orthodontic treatment. The aims of this in-vitro study were to investigate enamel damage depth on adhesive removal when the adhesive were surrounded by sound, demineralized or demineralized enamel that had been re-mineralized prior to adhesive removal using 10% Nano-Hydroxy apatite and to determine the effect of three different adhesive removal techniques. Materials and methods: Composite resin adhesive (3M Unitek) was bonded to 60 human upper premolars teeth which were randomly divided in to three groups each containing ten sound teeth and ten teeth with demineralized and re-mineralized lesions adjacent to the adhesive. A window of 2 mm was prepared on the bucca

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Publication Date
Tue Nov 25 2025
Journal Name
Journal Of Baghdad College Of Dentistry
Computed tomographic measurement of maxillary sinus volume and dimension in correlation to the age and gender (comparative study among individuals with dentate and edentulous maxilla)
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Background : Although development and progress in various diagnostic methods, but still identification of remnants of skeletal and decomposing parts of human is one of the most difficult skills in forensic medicine . Gender and age estimation is also considering an important problem in the identification of unknown skull. The aims of study: To estimate volume and dimension of maxillary sinus in individuals with dentate and edentulous maxillae using CT scan, and to correlate the maxillary sinus volume in relation to gender and age. Materials and Methods : This study included 120 patients ranged from (40-69 years), divided into two groups, dentate group with fully dentate maxilla and edentulous group with complete edentulous maxilla, and e

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