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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
Thu Jan 30 2020
Journal Name
Al-kindy College Medical Journal
Accuracy of Fine Needle Aspiration Biopsy (F.N.A.B) in Diagnosis of Breast Lump
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Background: Breast cancer is the first one among Iraqi females. Most of them present later for diagnosis. Early detection center in tertiary hospital practice uses FNAB for early diagnosis. Publications on accuracy of this detection are scarce.

Objective:  To test the accuracy of FNAB in breast lump diagnosis.

Methods: Diagnostic test accuracy study, on 204 women with breast lump, attending the oncology department in 2017.

Results: Fine-needle aspiration biopsy diagnosis of histologically malignant cases were, malignant in 89 (87.3%), suspicious of malignancy in 5 (4.9%), and benign in 4 (3.9%). Complete sensitivity was 87.3%, and specificity

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Publication Date
Fri Nov 15 2024
Journal Name
Iraqi Journal Of Science
Comparative Analysis for the Seasonal Variations of the IF2 and T Ionospheric Indices during Solar Cycles 23 and 24
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In this work, a comparative analysis for the behavior and pattern of the variations of the IF2 and T Ionospheric indices was conducted for the minimum and maximum years of solar cycles 23 and 24. Also, the correlative relationship between the two ionospheric indices was examined for the seasonal periods spanning from August 1996 to November 2008 for solar cycle 23 and from December 2008 to November 2019 for solar cycle 24. Statistical calculations were performed to compare predicted values with observed values for the selected indices during the tested timeframes. The study's findings revealed that the behavior of the examined indices exhibited almost similar variations throughout the studied timeframe. The seasonal variations were

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Publication Date
Tue Dec 09 2025
Journal Name
Journal Of Computer-aided Molecular Design
Synthesis, characterization and density functional theory of a novel dichloro(2-(1-anthracene-9-ylmethyl)-1H-1,2,3-triazole-5-yl) pyridine)Cu(II) and polymeric dichloro(2-(1-anthracene-9-ylmethyl)-1H-1,2,3 -triazole-5-yl)pyridine) Cd(II) complexes
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Publication Date
Thu Mar 25 2021
Journal Name
Modern Sport
The effect of physical exertion training using a vertimax device in developing the characteristic strength with speed and the skill of shooting by jumping in front - high with the hand ball for youth
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The research problem has crystallized and in light of these capabilities, the level of performance depends on the application of modern training methods based on actual experimentation, and those methods aim to develop the components of achievement in this competition, including the quantities of exerting the distinctive strength with speed for the arms and feet, which reflects on good skillful performance because the skill of shooting by jumping forward and high forms A major role in achieving goals during the competition that qualifies the team to win, and through the follow-up of the researcher in the field and academic field, I noticed that there is a weakness in some physical abilities, which affects performance and skill level

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Publication Date
Mon Jun 19 2023
Journal Name
Journal Of Engineering
A STUDY OF THE EFFECT OF SEMI-ANGLE OF CONE ON THE VIBRATION CHARACTERISTICS OF CYLINDRICAL-CONICAL COUPLED SHELL STRUCTURE
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In this work, the effect of variation of semi-angle of the conical part on the vibration characteristics of cylindrical-conical coupled structure is investigated. The shell is made of polyester resin reinforced by continuous E-glass fibers. The case is analyzed experimentally and numerically for orthotropic shell structures. The experimental program is conducted by exciting the fabricated structure by an impact hammer and monitoring the response using an attached accelerometer for different semi-angles of the conical part.
Software named SIGVIEW is used to perform the signal processing on the acquired signal in order to measure the natural frequencies and the corresponding mode shapes. The numerical investigation is achieved using ANS

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Publication Date
Fri Apr 01 2016
Journal Name
Al–bahith Al–a'alami
Journalism of Paper Newspapers in Light of the Competition of the Electronic Press / (A Field Study of Yemeni Daily Newspapers)
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The researcher seeks to get scientific facts through knowing the relationship between the priorities of Yemeni audience in follow-up paper daily newspapers compared to surfing publics the online journalism sites and the nature of information obtained from online journalism sites and printed paper newspapers and the impact of the daily newspapers in the priority of issues and political events among a sample of a group of Yemeni readers in order to identify the extent to keep up the paper daily newspapers of the development in the field of online journalism and the extent of reading paper newspapers under the intense competition by online journalism sites, and are paper newspapers able to keep pace with the actual developments provided by

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Publication Date
Sun Jun 04 2017
Journal Name
Baghdad Science Journal
Estimating of Fatty Acids, Tcopherols, Tocotrienols, Total Carotens, Study The Physiochemical Properties And Unsaponifiable Matters Extraction From Crude Red Palm Oil(1)
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The percentage of fatty acids, quantity of tocopherols, tocotrienols, carotens and physiochemical characteristics of crude red palm oil have been evaluated, in addition to specific chemical detection of active compounds unsaponifiable matters. Results of Gas Liquid Chromatography showed:- The major fatty acids in red palm oil is palmitic (44.36%) then oleic (39.65%), linolenic (10.55%), stearic (3.56%), myristic (1.22%), arachdonic (0.24%) and palmotic (0.19%). Red palm oil contains ? – ?- ?- ? – Tocopherols with concentration 258 , 121 , 259, 109 m/kg oil , ? – ?- ?- ? – Tocotrienol with concentration 462.77 , 571.03, 619.18, 509.07 m/kg oil respectively. Total tocopherols & tocotrienols 2909.05 m/kg oil and

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Publication Date
Wed Dec 09 2015
Journal Name
Iraqi Journal Of Market Research And Consumer Protection
Effect of Sodium sulfite treatment on the trypsin inhibitors activity, protein isolate and protein solubility of complete and dehulling white bean seeds Phaseolus vulgaris.: Effect of Sodium sulfite treatment on the trypsin inhibitors activity, protein isolate and protein solubility of complete and dehulling white bean seeds Phaseolus vulgaris.
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The study aimed to increase the biological value of white bean. The effect of different concentrations 0.01 ,0.02,0.03,and 0.04 M of sodium sulfite solutions for 1hr at 70 ºC on the trypsin inhibitors activity, protein isolate and protein solubility of complete and dehulling white bean flour were studied.Trypsin inhibitors activity were reduced by 42.97, 58.69, 68.59 and 69.58% in complete white bean flour at 0.01 ,0.02, 0.03, 0.04 M respectively, while the corresponding values were 50.43, 61.00, 75.61 and 85.66% respectively in dehulling white bean flour .Protein isolate value was 13.41% and protein solubility was 2.2% in control sample, Furthermore, the using of chemical treatment showed that protein isolate was reduced gradually and

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Publication Date
Thu Jul 01 2021
Journal Name
Energy
Experimental investigations of the performance of a flat-plate solar collector using carbon and metal oxides based nanofluids
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Publication Date
Thu Mar 31 2022
Journal Name
Journal Of The College Of Education For Women
Evaluating Teacher Preparation Programs in Scientific Disciplines at the Faculty of Education in Al-Aqsa University in Light of the Requirements of the Labor Market
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The current study seeks to evaluate teacher preparation programs in the scientific disciplines at the College of Education in Al-Aqsa University in the light of the requirements of the labor market. It further aims to reveal the significance of the differences in the sample members’ response averages of to the availability of labor market requirements in the program that prepares the teacher of scientific disciplines at the Faculty of Education in Al-Aqsa University taking into account the (gender, program) variables. The study followed the descriptive analytical approach, and so a questionnaire was distributed to a sample of scientific discipline students in the teacher preparation program adopted in Al-Aqsa University, (200) male and

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