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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 Oct 20 2018
Journal Name
Journal Of Economics And Administrative Sciences
Fluctuations of global crude oil prices and their effect on inflation and economic growth in Iraq " A standard study for the period 1988– 2015
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Abstract

That Iraq's dependence on the revenues of the oil product in financing its development programs and growth rates , Making the economy affected by external forces represented by fluctuations in crude oil prices in the global market, Which is directly reflected on the performance and efficiency of the Iraqi economy.

The study adopted its objectives to analyze the time series for the period (1988 - 2015) through the use of standard and statistical methods, Four standard models were estimated to reach those targets, Where the results of the stability test showed instability of most variables at their original level, But to achieve stability when taking the first differences, While the result

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Publication Date
Fri Mar 01 2024
Journal Name
Baghdad Science Journal
Study the Structural Properties of Porous Silicon and their Applications as Thermal Sensors
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The photo-electrochemical etching (PECE) method has been utilized to create pSi samples on n-type silicon wafers (Si). Using the etching time 12 and 22 min while maintaining the other parameters 10 mA/cm2 current density and HF acid at 75% concentration.. The capacitance and resistance variation were studied as the temperature increased and decreased for prepared samples at frequencies 10 and 20 kHz. Using scanning electron microscopy (SEM), the bore width, depth, and porosity % were validated. The formation of porous silicon was confirmed by x-ray diffraction (XRD) patterns, the crystal size was decreased, and photoluminescence (PL) spectra revealed that the emission peaks were centered at 2q of 28.5619° and 28.7644° for et

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Publication Date
Sat Jul 18 2020
Journal Name
College Of Islamic Sciences
Methodology of Bible Criticism of Muslim Scholars in South Africa Ali Safraz Khan Gumal as a sample
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This paper and research paper analyzes the critical methodology of "Ali Khan Joommal “ about the Bible , directed in most of the textual criticism of the Torah, and its highest criticism is directed to both the Old and New Testaments.

Joommal  was distinguished by the mental methods and examples accompanying his era, while maintaining the general context in which Muslim scholars had previously followed, and he was distinguished from them by his many citations to the Western literature of Jews or Christians, in short it is a critical phenomenon worthy of study and evaluation.

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Publication Date
Fri Sep 30 2016
Journal Name
Iraqi Journal Of Science
Anti-Mullerian Hormone and Follicle Stimulating Hormone as Markers of Ovarian Agingin a Sample of Iraqi Women
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One-hundred and twenty Iraqi women (60 single women and 60 married women) with age ranges from (17-49) years have been involved in this study to estimate the levels of anti-mullerian hormone (AMH) and follicle stimulating hormone (FSH) as markers of ovarian aging. The descriptive data [age, body mass index (BMI), age at menarche, duration of menarche] have been recorded. Blood samples were collected from the studied women to determine the levels of AMH and FSH. The results revealed non-significant (p>0.05) differences in levels of AMH and FSH between single women and married women. A significant negative correlation was observed between AMH levels and age in single women (r=-0.519, p<0.05) and married women (r=-0.433, p<0.05). A no

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Publication Date
Thu Mar 30 2017
Journal Name
Iraqi Journal Of Pharmaceutical Sciences ( P-issn 1683 - 3597 E-issn 2521 - 3512)
Synthesis and Preliminary Pharmacological Evaluation of Aminobenzensulfonamides Derivatives of Mefenamic Acid as a Potential Anti-inflammatory Agents
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A group of amino derivatives [4-aminobenzenesulfonamide,4-amino-N¹ methylbenzenesulfonamide, or N¹-(4-aminophenylsulfonyl)acetamide] bound to carboxyl group of mefenamic acid a well known nonsteroidal anti-inflammatory drugs (NSAIDs) were designed and synthesized for evaluation as a potential anti-inflammatory agent.  In vivo acute anti-inflammatory activity of the final compounds (9, 10 and 11) was evaluated in rat using egg-white induced edema model of inflammation in a dose equivalent to (7.5mg/Kg) of mefenamic acid. All tested compounds produced a significant reduction in paw edema with respect to the effect of propylene glycol 50% v/v (control group). Moreover, the 4-amino-N-methylbenzenesulfonamide derivative (c

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Publication Date
Wed Aug 30 2023
Journal Name
Baghdad Science Journal
Impact of COVID-19 Vaccine on Hearing Status of Young Ages (Medical College Students as a Sample)
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Many studies dealt with the consequences of  SARS CoV-2  (which cause COVID-19 infection) on the nervous system especially sensory nerves where the virus causes loss of taste and smell as it’s known, and may affect auditory nerves and be the expected cause of some hearing problems. A case-control analytic study was performed on a connivance sample of society of university students from a medical faculty. Each participant filled out a questionnaire contains demographic data and general, auditory and respiratory health condition, in addition to vaccination status. In the other side, the audio- examinations were performed on the study sample including Pure Tone Audiometry (PTA) and tympanometry. Two statistical methods; chi-square and t

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Publication Date
Sun Jul 01 2001
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
New record of ground pearls, Porphyrophora tritici (Bod.) (Homoptera, Margarodidae) as a pest of wheat in Iraq
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The ground pearls, Porphyrophora tritici (Bod.) is a new insect pest on wheat recorded for
the first time from Mousl Province, North of Iraq.

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Publication Date
Tue Jan 08 2019
Journal Name
Iraqi Journal Of Physics
Effect of concentrations ratios of NiO on the efficiency of solar cell for (CdO)1-x(NiO)x thin films
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CdO:NiO/Si solar cell film was fabricated via deposition of CdO:NiO in different concentrations 1%, 3%, and 5% for NiO thin films in R.T and 723K, on n-type silicon substrate with approximately 200 nm thickness using pulse laser deposition. CdO:NiO/n-Si solar cell photovoltaic properties were examined under 60 mW/cm2 intensity illumination. The highest efficiency of the solar cell is 2.4% when the NiO concentration is 0.05 at 723K.

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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 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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