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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 Dec 24 2022
Journal Name
Research Journal Of Pharmacy And Technology
Biological Study of protease produced by clinical isolates of Staphylococcus aureus
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The bacterial isolates were obtained from Al-Kindi Hospital were diagnosed by the Vitek-2 system and re confirm by 16srRNA gene as S. aurous, the results were shown 20 isolates (66.7%) out of 30 isolates were positive to protease production. All bacterial isolates (100%) were sensitive to Gentamicin and Levofloxacin. but resistant (100%) to aztreonam. The best temperature for enzyme production from bacteria was 37 °C, and the best pH for enzyme production was 7. Partial purification of the bacterial enzyme (protease) was carried out using short steps included ammonium sulfate 65% saturation, ion exchange using DEAE- cellulose column and then applied on gel filtration chromatography using Sephadex G-200 column. The enzymatic activit

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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
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
Thu Nov 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
The role of compensation system in improving the quality of educational services (Halabja University as a model)
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          This study deals with the role of compensation system in improving the quality of educational services (University of Halabja as a Model) also our problem was the following question ; What is the role of compensation system in its different dimensions in improving the quality of educational services? And what is the relationship and impact of using the dimensions of the compensation system to improve the quality of educational services? The hypothesis of the research included the correlation and the impacts between the compensation system and its combined variables in the quality of educational services. This was proved through a field study and the distribution of questionn

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Publication Date
Sun Sep 07 2014
Journal Name
Baghdad Science Journal
A comparative taxonomic study of nutlets of Stachys L. in Iraq
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Nutlets of 22 taxa of Stachys (13 species and seven subspecies and two varieties), representing seven of the currently recognized sections distributed in northern Iraq were examined by light microscope. The basic shape of nutlets in most taxa studied is Obovoid, but Oblong also found in S.megalodanta Hausskn.& Bornm. ex P.H.Davis, S.setirefa C.A.Mey. subsp daenensis (Gandog.) Rech.f.and S. kurdica Boiss.& Hohen. var.kurdica, while the Subgloboid shape found in S. iberica M.Bieb. and S. inflata Benth., more over the Broad triangular shape was found in S. nephrophylla Rech.f. and S.lanigera (Bornm.) Rech.f.., the biggest size of nutlets was found in S.inflata L. and the smallest was in S.melampyroides Hand.-Mzt. Regarding sculpturing pa

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Publication Date
Sun Mar 15 2020
Journal Name
Journal Of The College Of Education For Women
The Use of English as Lingua Franca in the Classes of UKM: as A Case of Study
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           English has for long been one of the most widely used media of communication globally, especially in the Malaysian universities. It has been termed as a Lingua Franca because it is shared with other languages which are considered first languages by different speakers. For this reason, English as a Lingua Franca (ELF) has attracted a number of researchers to investigate its variety via other languages in various communities. The objective of this paper is therefore to establish the strategies which are employing by the international students at the National University of Malaysia/ UniversitiKebangsaan Malaysia (UKM) as an example of one of the Malaysian universities; when they e

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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
Tue Oct 01 2024
Journal Name
Journal Of Engineering Science And Technology
NUMERICAL SIMULATION OF SHEET PILES AS A SEEPAGE CUTTER OFF: AL-KIFIL REGULATOR AS A CASE STUDY
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Sheet piles are necessary with hydraulic structures as seepage cut-off to reduce the seepage. In this research, the computational work methodology was followed by building a numerical model using Geo-Studio program to check the efficiency of using concrete sheet piles as a cut-off or reducer for seepage with time if the sheet piles facing the drawdown technique. Al-Kifil regulator was chosen as a case study, an accurate model was built with a help of observed reading of the measuring devices, which was satisfactory and helped in checking the sheet piles efficiency. Through the study, three scenarios were adopted (with and without) drawdown technique, it was found that at the short time there's no effect of the drawdown technique on

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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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Publication Date
Tue Jun 16 2020
Journal Name
Synthetic Communications
Synthesis, identification and molecular docking studies of N-functionalized piperidine derivatives linked to 1,2,3-triazole ring
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