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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
Sun Jun 01 2014
Journal Name
مجلة كلية مدينة العلم الجامعة
Palynological study for nine cultivated species of Asteraceae family
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The current research included palynological study for nine ornamental cultivated species of Asteraceae family. The study included measurement the dimensions of pollen grains and there shape in polar view and equatorial view, sculpturing,colpi length and width, spines length and number of spines rows between colpiand exine thickness, the study showed variations in pollen grains characters forthe studied taxa

Publication Date
Sat Dec 31 2016
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Performance Study of Electrodialysis for Treatment Fuel Washing Wastewater
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In this work, electrodialysis (ED) has been demonstrated to be appropriate technique for reducing the electrical conductivity of real wastewater from fuel washing unit, which has been previously treated by other electrochemical technology (electrocoagulation and electrooxidation).  A five cell electrodialysis stack, with an active membrane area of 60 cm2 per cell was employed. During a batch recirculation mode ED system, the effects of parameters such as electrical potential applied (6-18 V) and flow rate of streams (0.5-1.7 L/min.) on the performance of the total dissolved solids (TDS) separation and specific power consumption (SPC) were studied. The results indicate that the process of ED under potential (15 V) and flow

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
(?m 10.6) Design study for Reserve of laser CO2
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In this paper , the CO2 laser receiver system is designed and studied, with wavelength laser 10.6 ?m in room temperature , and to evaluate the performance and discussion it via the package of optical design (ZEMAX), from its output the Spot Diagram is measured through RMS ,and from the Ray fan plot , the aberrations is found which is the normal error for the best focus named (under corrected ) , the other output was the Geometric Encircled Energy in the spot diagram . and found that the radius of spot diagram at 80% (R80%) from the total energy ,and focal shift .The designed system have high efficiency and low cost .

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Publication Date
Wed Jan 08 2025
Journal Name
Journal Of Al-rafidain University College For Sciences ( Print Issn: 1681-6870 ,online Issn: 2790-2293 )
Utilizing the Error Correction Model to Investigate the Impact of Fluctuations in Bank Deposits on the Money Supply
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This paper assesses the impact of changes and fluctuations in bank deposits on the money supply in Iraq. Employing  the research constructs an Error Correction Model (ECM) using  monthly time series data from 2010 to 2015. The analysis begins with  the Phillips-Perron unit root test to ascertain the stationarity of the  time series and the Engle and Granger cointegration test to examine  the existence of a long-term relationship. Nonparametric regression functions are estimated using two methods: Smoothing Spline and M-smoothing. The results indicate that the  M-smoothing approach is the most effective, achieving the shortest adjustment period and the highest adjustment ratio for short-term disturbances, thereby facilitating a return

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Analyzing the impact of exchange rate fluctuations and inflation on the GDP in Iraq using the modern methodology of Cointegration for the period (1988-2020)
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     The research aims to analyze the impact of exchange rate fluctuations (EXM and EXN) and inflation (INF) on the gross domestic product (GDP) in Iraq for the period 1988-2020. The research is important by analyzing the magnitude of the macroeconomic and especially GDP effects of these variables, as well as the economic effects of exchange rates on economic activity. The results of the standard analysis using the ARDL model showed a long-term equilibrium relationship, according to the Bound Test methodology, from explanatory (independent) variables to the internal (dependent) variable, while the value of the error correction vector factor was negative and moral at a level less than (1%). The relationship bet

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Publication Date
Tue Feb 05 2019
Journal Name
Journal Of The College Of Education For Women
The effect of teaching using the six thinking hats on academic achievement for students in the second grade average in the subject of family education
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Research problem:
Problem of current research can determine the dimensions to answer the following question: The effect of teaching using the six thinking hats on academic achievement for students in the second grade average in the subject of Family Education. The importance of research: research is gaining importance in terms of:
1. That this research is the first of its kind in the researcher's knowledge _ which deals with the teaching of Family Education by using the six hats, the researcher hopes to fill a gap in the educational field and serve in other studies serve the materials home economics. 2. Keep pace with the new field of modern education and strategies. 3. Highlight on the educational strategy in the field of creative

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Publication Date
Mon Jun 13 2022
Journal Name
International Journal Of Health Sciences
Iraqi EFL teachers, supervisors and students’ perception of CLT principles and practices at Iraqi schools: A study of its benefits, snags, and future directions
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Even though in recent decades a bulk of studies have been accomplished on the use of communicative language teaching (CLT) in English as a foreign language (EFL) environments, fairly a limited numbers of studies precisely dealt with investigating the attitudes of language teachers, students and supervisors concerning the principals of CLT in the context of Iraq. Henceforth, this study was designed to delve into the attitudes of teachers, learners and supervisors about the implementation. To this end, the study was accomplished using a mixed method design. The present study was carried out in two phases: designing and using a questionnaire plus interviewing the teachers, students and supervisors (51 language learners, 41 teachers and

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Publication Date
Thu Sep 24 2020
Journal Name
F1000research
Characterization of flow cytometric immuno-phenotyping of acute myeloid leukemia with minimal differentiation and acute T-cell lymphoblastic leukemia: A retrospective cross-sectional study
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Background: Acute leukemias (ALs) are a heterogeneous group of malignancies with various clinical, morphological, immunophenotypic, and molecular characteristics. Distinguishing between lymphoid and myeloid leukemia is often performed by flow cytometry. This study aimed to evaluate the immunophenotypic characterization and expression of immuno-markers in both acute myeloid leukemia (AML-M0) and acute T-cell lymphoblastic leukemia (T-ALL).

Methods: A retrospective cross-sectional study was conducted in the Pathology Department/Teaching Laboratories/Medical City/Iraq and included all patients newly diagnosed with AL from 5 January to 10 December 2018. Immunophenotypic analysis wa

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Publication Date
Wed Oct 30 2024
Journal Name
Iraqi Journal Of Science
Evaluation of the Activity of Olibanum Oil as an Immune Booster in Rats
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The applications of herbal medicine have recently acquired growing interest in range of the prophylaxis and treatment of diseases. Olibanum has been used since ancient eras and several reports studied the pharmacological characteristics of boswellic acid, particularly their effect on the inflammatory response, analgesic properties, and anti-arthritic activity mostly in cell lines, but new approaches include animal models to assess these natural derivatives effects taking into consideration of being safer than synthetic preparations.  The impact of olibanum oil on several parameters was studied in rats during this study. These included white blood cell (WBC) count, lactate dehydrogenase (LDH), and C reactive protein (CRP), as well a

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Publication Date
Mon Sep 23 2019
Journal Name
Baghdad Science Journal
Representation of Algebraic Integers as Sum of Units over the Real Quadratic Fields
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In this paper we generalize Jacobsons results by proving that any integer  in   is a square-free integer), belong to . All units of  are generated by the fundamental unit  having the forms

our generalization build on using the conditions

This leads us to classify the real quadratic fields  into the sets  Jacobsons results shows that  and Sliwa confirm that  and  are the only real quadratic fields in .

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