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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 28 2023
Journal Name
Research Journal Of Pharmacy And Technology
Synthesis and Characterization of Molecularly Imprinted Polymers for Metronidazole by using Allyl Chloride and Allyl Bromide as Monomers
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Metronidazole-MIPs were prepared by using (MDZ) as the template as well as allylchloride (AYC) or allylbromide (AYB) as monomer, used (TMPTA) tri-methylol propane tri-acrylate or ethylene glycol di-methyl acrylate (EGDMA) as cross-linker and initiator used (BP) benzyl peroxide. By using different plasticizers (di butyl Phthalate (DBPH), Nitrobenzene (NB), oleic acid (OA) and paraffin) for MDZ-MIP1 and (Di-butyl sebecate (DBS), Di-methyl acrylate (DMA), Tributylphosphate(TBP) and Tris(ethylhexyl phosphate (TEHP) ) for MDZ-MIP2. Membranes of MIPs were prepared in PVC matrix. The characterizations of each electrode were determined The Slope range from (55.083 - 43.711) mV/decade, Limit of Detection (8 X 10 -4- 2 X 10-6) and Linearity

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Publication Date
Sat Aug 01 2020
Journal Name
Heat Transfer
A parametric study of a photovoltaic panel with cylindrical fins under still and moving air conditions in Iraq
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Publication Date
Sat Dec 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Organizational Tactics An Approach to Strategic Agility A field study in a sample of mobile operators in Iraq
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The current research dealt with the issue of organizational skillfulness as an entry point to reach strategic agility. The study has been tested in Iraq's mobile operators - Asia Cell, Zain Iraq and Cork Telecom. The study was applied to a sample of (93) managers distributed at various levels of management (board members, general managers, commissioners, department managers, people managers, unit managers, office managers). The survey used the questionnaire as a key tool for collecting data and information as well as personal interviews. It has sought to test a number of hypotheses related to correlation and influence relationships between the variables of the study, in order to answer the questions related to the problem of stud

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Publication Date
Fri Mar 15 2024
Journal Name
Journal Of Baghdad College Of Dentistry
A clinicopathological analysis of 151 odontogenic tumors based on new WHO classification 2022: A retrospective cross-sectional study
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Background: Odontogenic tumors are a diverse group of lesions with a variety of clinical behavior and histopathologic subtypes, from hamartomatous and benign to malignant. The study aimed to examine the clinical and pathological features of odontogenic tumors in Baghdad over the last 11 years (2011–2021). Materials and Methods: The present retrospective study analyzed all formalin-fixed, paraffin-embedded tissue blocks of patients diagnosed with an odontogenic tumor that were retrieved from archives at a teaching hospital/College of Dentistry in Baghdad University, Iraq, between 2011 and 2021. The diagnosis of each case was confirmed by examining the hematoxylin and eosin stained sections by two expert pathologists. Data from pati

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Publication Date
Sat Feb 09 2019
Journal Name
Journal Of The College Of Education For Women
The women at Al-Sakhaawi Book "A;-Dhau Al-Lami", Study in the social life
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In our previous research , we study the method of women by ( al – sakhaawi " died 902
ah/1496a.c"book witch called ( al- dhau, al-lami) .
So in this paper , we will discuss the social life of women in the mamluk period through the
same book ,especially when the sakhaawi devoted a full part for women in the same book
called it (mhagam ,al –nessa)wich it translations a large number of women like wives
,daughters ,sisters ,and maids of mamluk sultans ,so that make my able to know a lot about
the social life of woman which we study it like a social aspects of women, here wealth,
business, professions ,and in the last we study the habits of them marriage .

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Publication Date
Fri Dec 20 2019
Journal Name
College Of Islamic Sciences
The role of a teacher of Islamic education In explaining the concepts of political freedom Educational guidance study
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The political struggle being waged by Muslims today is one of the most important issues that have preoccupied the Arab and international media, and the failures that have afflicted Muslims in our contemporary world have negatively affected the younger generations and led them, and with the influence of anti-Islam media, to rely on accusing Islam as a religion with all the negative in Islamic and Arab society . So secularism took its role in spreading these concepts by deviating from its course from the concept of science to the concept of (the religion).
    From here the calls for reform rose to return the Muslims to the incubator of Islam, so people turned around them, but they turned into competing Islamic polit

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Publication Date
Tue Jun 01 2021
Journal Name
Political Sciences Journal
The role of elections in solidifying the process of democratization: a case study of Tunisian elections in 2019
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The electoral mechanism is remarkably clear, a political tool for institutional construction, directing political life, forming the political scene, and forming the partisan scene. This process was through the design of electoral laws, as elections in Tunisian political history represented the indicator of its slow and accelerated transformations, so The elections in Tunisia usually coincide with important political stages, accompanied by legislative or constitutional amendments in general, Islamic or secular forces have played a fundamental role in promoting the democratic experience and the principle of the peaceful transfer of power. This led to the formation of a national consensus that would help the country not enter into political

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Publication Date
Sun Jan 01 2017
Journal Name
البحوث التربويةوالنفسية
Preparing a teacher’s guide for computer books for the intermediate stage according to learning styles
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Publication Date
Thu Apr 01 2021
Journal Name
Biochemical And Cellular Archives
STUDY OF LYSYL OXIDASE-1 AND KIDNEY FUNCTION IN SERA OF IRAQI PATIENTS WITH DIABETIC NEPHROPATHY
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This study aimed to compare lysyl oxidase-1 level in diabetic patients with and without renal dysfunction, that LOX-1 may be an indicator for the early stage of diabetic nephropathy (DN). In addition to finding it is a relationship with kidney functions in Iraqi diabetic patients with and without renal dysfunction. Blood was obtained from 25 healthy individuals as a control group (G1), 25 diabetic patients with renal dysfunction, and 25 diabetic patients without renal dysfunction. Age range 40-60 years for all subjects. BMI (25-27) Kg/m2 . The serum was used for the analysis of LOX-1, FBG, urea, creatinine and uric acid. Whole blood is used for the determination of HbA1C. Results of FBG and HbA1C revealed a significant increase in G2 and G

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Publication Date
Wed Apr 01 2020
Journal Name
Isa Transactions
Design of a Complex fractional Order PID controller for a First Order Plus Time Delay system
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