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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
Fri Dec 15 2023
Journal Name
Iraqi Journal Of Laser
Study the Impact of Silica Nanoparticles on the Properties of Several Dyes for the Fabrication of a Random Laser Gain Medium
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Random laser gain media is synthesized with different types of dye at the same concentration (1×10-3 M) as an active material and silicon dioxide NPs (silica SiO2) as scatter centers through the Sol-Gel technique. The prepared samples are tested with UV–Vis spectroscopy, Fluorescence Spectroscopy, Field Emission Scanning Electron Microscopy (FESEM), and Energy Dispersive X-ray Diffraction (EDX). The end result demonstrates that doped dyes with silica nanoparticles at a concentration of 0.0016 mol/ml have lower absorbance and higher fluorescence spectra than pure dyes. FESEM scans revealed that the morphology of nanocrystalline silica is clusters of nano-sized spherical particles in the range (25-67) nm. It is con

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Publication Date
Sat Feb 09 2019
Journal Name
Journal Of The College Of Education For Women
A Study of the Problems of Learning and Translating Idioms
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Idioms are a very important part of the English language: you are told that if you want to go far (succeed) you should pull your socks up (make a serious effort to improve your behaviour, the quality of your work, etc.) and use your grey matter (brain).1 Learning and translating idioms have always been very difficult for foreign language learners. The present paper explores some of the reasons why English idiomatic expressions are difficult to learn and translate. It is not the aim of this paper to attempt a comprehensive survey of the vast amount of material that has appeared on idioms in Adams and Kuder (1984), Alexander (1984), Dixon (1983), Kirkpatrick (2001), Langlotz (2006), McCarthy and O'Dell (2002), and Wray (2002), among others

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Publication Date
Sun Mar 01 2015
Journal Name
Current Research In Microbiology And Biotechnology
Evaluation for the Cytotoxic Effect of Exotoxin A Produced by Pseudomonas aeruginosa on Mice by using Cytogenetic Parameters
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This research was conduct to evaluate the cytotoxic effect of exotoxin A (ETA) produced by Pseudomonas aeruginosa on mice in comparison with (phosphate buffer saline (PBS) as a negative control. The effect of the toxin was measured by employing the cytogenetic analysis which included (the mitotic index (MI), chromosomal aberrations (CAs), micronucleus (MN) and sperm abnormalities) parameters. In order to specify the cytotoxic effect of the toxin, three doses of ETA (125, 250 and 500 ng/ml) were used. Results showed that ETA was found to cause a significant decrease in mitotic index (MI) percentage, while significant increase in micronucleus (MN), chromosomal aberrations (CAs) and sperm abnormalities parameters in compression with control wa

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Publication Date
Wed Mar 30 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Crystallization Process as a Final Part of Zero Liquid Discharge System for Treatment of East Baghdad Oilfield Produced Water
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This study investigated the application of the crystallization process for oilfield produced water from the East Baghdad oilfield affiliated to the Midland Oil Company (Iraq). Zero liquid discharge system (ZLD) consists of several parts such as oil skimming, coagulation/flocculation, forward osmosis, and crystallization, the crystallization process is a final part of a zero liquid discharge system. The laboratory-scale simple evaporation system was used to evaluate the performance of the crystallization process. In this work, sodium chloride solution and East Baghdad oilfield produced water were used as a feed solution with a concentration of 177 and 220 g/l. The impact of temperature (70, 80, and 90 °C), mixing speed (300, 400, and 500 rp

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Publication Date
Wed Mar 30 2022
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Crystallization Process as a Final Part of Zero Liquid Discharge System for Treatment of East Baghdad Oilfield Produced Water
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This study investigated the application of the crystallization process for oilfield produced water from the East Baghdad oilfield affiliated to the Midland Oil Company (Iraq). Zero liquid discharge system (ZLD) consists of several parts such as oil skimming, coagulation/flocculation, forward osmosis, and crystallization, the crystallization process is a final part of a zero liquid discharge system. The laboratory-scale simple evaporation system was used to evaluate the performance of the crystallization process. In this work, sodium chloride solution and East Baghdad oilfield produced water were used as a feed solution with a concentration of 177 and 220 g/l. The impact of temperature (70, 80, and 90 °C), mixing speed (300, 400, and 500

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Publication Date
Tue Dec 01 2020
Journal Name
Journal Of Economics And Administrative Sciences
The possibility using of Accounting Information in Rationalizing the Decisions of Capital Expenditure (A case study: Companies Listed in Khartoum Stock Exchange)
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The research aims at the identity of the accounting information and its characteristics, and then to study the possibility of using accounting information in rationalizing the decisions of capital expenditure. The study relied upon the descriptive analytical approach it is suitable to the nature of this study, the hypotheses of the study were tested by using a number of statistical methods by relying on statistical package program (SPSS), and the research concluded that the companies listed in Khartoum Stock Exchange using accounting information in the comparison between investment alternatives available and estimating the number of years required to recover of the investment cost, the challenges that cause weakness in using the

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Publication Date
Mon Jun 23 2025
Journal Name
Journal Of Craniofacial Surgery
Gender Determination in Forensic Dentistry Using Bonwill’s Triangle Measurements From CBCT Scans: A Study on the Iraqi Population
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Background:

The purpose of this study is to illuminate the role of CBCT in forensic dentistry through variations of mandibular measurements of Bonwill’s triangles in gender determination among the Iraqi population.

Materials and methods:

In this retrospective study 70 CBCT scans were analyzed to measure the Bonwill’s triangle, 35 for males and 35 for females aged between 20 and 50 years, all data were collected at the oral and maxillofacial radiology department in Ghazi AL-Hariri hospital for 3 months, and the data were obtained using a Kavo CBCT device (3D On De

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Publication Date
Wed May 31 2023
Journal Name
International Journal Of Advanced Technology And Engineering Exploration
Investigation of phase change characteristics for refrigerant R-134a flow in a double pipe heat exchanger with the use of thermal non-equilibrium model
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Almost all thermal systems utilize some type of heat exchanger. In a lot of cases, evaporators are important for systems like organic Rankine cycle systems. Evaporators give a share in a large portion of the capital cost, and their cost is significantly attached to their size or transfer area. Open-cell metal foams with high porosity are taken into consideration to enhance thermal performance without increase the size of heat exchangers. Numerous researchers have tried to find a representation of the temperature distribution closer to reality due to the different properties between the liquid and solid phases. Evaporation heat transfer in an annular pipe of double pipe heat exchanger (DPHEX) filled with cooper foam is investigated numerical

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Publication Date
Wed Jun 07 2023
Journal Name
Journal Of Educational And Psychological Researches
A Proposed Training Program for School Leaders in the Sultanate of Oman on the Planning Practices of the Kaufman Model in Light of the Needs and Challenges of Reality
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The study aims to build a proposed training program for school leaders in the Sultanate of Oman on the planning practices of the Kaufman model in light of the needs and challenges of reality. It also aims to identify the challenges facing school leaders in practicing the stages of strategic planning. To achieve these objectives, the study adopted the descriptive approach due to its suitability to the nature of the study. A questionnaire was used to collect the needed data. The study sample included (225) individuals from school principals, their assistants and senior teachers in post-basic education in the Sultanate of Oman. After processing the data statistically, the study concluded that the reality of planning practices for school lea

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Publication Date
Sun Mar 01 2015
Journal Name
Baghdad Science Journal
A New method for ISE construction for methyl orange dyes and using for indirect determination of Amitriptyline Hydrochloried drug
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A new method for construction ion-selective electrode (ISE) by heating reaction of methyl orange with ammonium reineckate using PVC as plasticizer for determination methyl orange and determination Amitriptyline Hydrochloried drug by formation ion-pair on electrode surface . The characteristics of the electrode and it response as following : internal solution 10-4M , pH (2.5-5) ,temperature (20-30) and response time 2 sec. Calibration response for methyl orange over the concentrationrange 10-3 -10-9 M with R=0.9989 , RSD%=0.1052, D.O.L=0.315X10-9 MEre%=(-0.877- -2.76) , Rec%.=(97.230 -101.711) .

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