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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 Jun 30 2023
Journal Name
حوليات اداب عين شمس
Names of Day of Resurrection in the Hebrew translation of the meanings of the Holy Quran An analytical study Uri Rubin translation as a model
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The present study discusses the names of the Day of Resurrection in Uri Rubin’s translations of the Holy Qur’an. To identify the translation difficulties and complications and to find out the Hebrew equivalence, the study, through the application of a comparative analytical approach, aims at analyzing the linguistic structures of Day of Resurrection names cited in the Holy Qur’an. Heavenly religions are rich with distinct and unique terms that distinguish and reflect their specificity of other religions; something requires a great accuracy in the translation of such terminology. By investigating selected examples of the names of the Day of Resurrection in Arabic and Hebrew, the present study sheds light on the morphological and semant

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Publication Date
Fri Jul 01 2016
Journal Name
Al–bahith Al–a'alami
Manufacturing the Functions and Responsibilities of the Press Photo: The Photo of the Child Elian as a Model
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The theory of the psychologist’s Piaget states that man passes through four stages; other says that mankind passes through five. At each stage, human learn new characteristics, values, skills, and cultures from different environment that differ from one society to another. Therefore, the cultures of societies vary according to the diversity of the environments. These environments also vary depending on the circumstances surrounding them, e.g., in war environment, the individual learns what he does not learn from living in safe environment. As the environment changes, the communicative message also changes. This message is subject to person, groups, organizations and parties and directed to a diverse audience in its orientations and bel

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Publication Date
Tue Jul 01 2025
Journal Name
Minerva Dental And Oral Science
Evaluation of the microleakage of new bioactive restorative materials: a comparative in-vitro study
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Publication Date
Wed May 31 2023
Journal Name
International Journal Of Sustainable Development And Planning
Prediction of Formal Transformations in City Structure (Kufa as a Model) Based on the Cellular Automation Model and Markov Chains
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The research utilizes data produced by the Local Urban Management Directorate in Najaf and the imagery data from the Landsat 9 satellite, after being processed by the GIS tool. The research follows a descriptive and analytical approach; we integrated the Markov chain analysis and the cellular automation approach to predict transformations in city structure as a result of changes in land utilization. The research also aims to identify approaches to detect post-classification transformations in order to determine changes in land utilization. To predict the future land utilization in the city of Kufa, and to evaluate data accuracy, we used the Kappa Indicator to determine the potential applicability of the probability matrix that resulted from

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Publication Date
Sat Sep 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Performance of Electro-Fenton Process for Phenol Degradation Using Nickel Foam as a Cathode
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Toxic substances have been released into water supplies in recent decades because of fast industrialization and population growth. Fenton electrochemical process has been addressed to treat wastewater which is very popular because of its high efficiency and straightforward design. One of the advanced oxidation processes (AOPs) is electro-Fenton (EF) process, and electrode material significantly affects its performance. Nickel foam was chosen as the source of electro-generated hydrogen peroxide (H2O2) due to its good characteristics. In the present study, the main goals were to explore the effects of operation parameters (FeSO4 concentration, current density, and electrolysis time) on the catalytic performance that was optimized by r

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Publication Date
Sat Sep 30 2023
Journal Name
Iraqi Journal Of Chemical And Petroleum Engineering
Performance of Electro-Fenton Process for Phenol Degradation Using Nickel Foam as a Cathode
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Toxic substances have been released into water supplies in recent decades because of fast industrialization and population growth. Fenton electrochemical process has been addressed to treat wastewater which is very popular because of its high efficiency and straightforward design. One of the advanced oxidation processes (AOPs) is electro-Fenton (EF) process, and electrode material significantly affects its performance. Nickel foam was chosen as the source of electro-generated hydrogen peroxide (H2O2) due to its good characteristics. In the present study, the main goals were to explore the effects of operation parameters (FeSO4 concentration, current density, and electrolysis time) on the catalytic perform

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Publication Date
Mon Feb 01 2021
Journal Name
Iop Conference Series: Materials Science And Engineering
Azo Coupling Reaction for indirect Spectrophotometric Determination of Furosemide using Resorcinol as a Reagent
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Abstract<p>A simple and accurate method to determinate furosemide (FUR) based on converting the secondary amine to primary amine with acidic hydrolysis then azotization by nitrous acid and coupled with resorcinol as a coupling agent in aqueous medium at pH 13. The optical characteristic like beers law limit found to be (0.25-2.5) μg.ml<sup>−1</sup>, detection and quantification limits (0.0196) (0.0654) μg.ml<sup>−1</sup>respectivly and Sandel sensitivity was 0.006738 μg.cm<sup>−2</sup>. The least-square method was used to evaluate the regression equation and the correlation coefficient. The resulted azo dye has a maximum absorbance at 430 nm with light oran</p> ... Show More
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Publication Date
Tue Oct 01 2019
Journal Name
2019 12th International Conference On Developments In Esystems Engineering (dese)
Roadway Deterioration Prediction Using Markov Chain Modeling (Wasit Governorate/ Iraq as a Case Study)
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Publication Date
Wed Jun 01 2022
Journal Name
Journal Of Sport Science Technology And Physical Activities
The effect of using Daniel's model and Driver’s model in learning a kinetic chain on the uneven bars in the artistic gymnastics for female students
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The aim of this study to identity using Daniel's model and Driver’s model in learning a kinetic chain on the uneven bars in the artistic gymnastics for female students. The researchers used the experimental method to design equivalent groups with a preand post-test, and the research community was identified with the students of the third stage in the college for the academic year 2020-2021 .The subject was, (3) class were randomly selected, so (30) students distributed into (3) groups). has been conducted pretesting after implementation of the curriculum for (4) weeks and used the statistical bag of social sciences(SPSS)to process the results of the research and a set of conclusions was reached, the most important of which is t

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Publication Date
Tue Oct 25 2016
Journal Name
Iosr Journal Of Pharmacy And Biological Sciences
Molecular study of blaVEB-1 gene in Proteus mirabilis isolated from clinical Samples from Baghdad City’s hospitals
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From different hospitals in Baghdad city, 25 clinical isolates of Proteus spp. were collected from different clinical samples, all isolates were identified as Proteus mirabilis by using bacteriological and biochemical assays in addition to Vitek-2 identification system. 15 (60%) isolates were identifying as Proteus mirabilis. The susceptibility of P. mirabilis isolates towards cefotaxime and ceftazidime was (66.6 %), (20%) consecutively; while extended spectrum β-lactamases producing P. mirabilis percentage was (30.7 %). Because blaVEB-1 was documented as an important indicator for increasing risk of extended spectrum beta ßlactamases producing P. mirabilis isolates that began to spread from many geographic area to Far east which inc

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