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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
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
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
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 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
Thu Oct 15 2020
Journal Name
International Journal Of Energy Research
Mixed-ligand complexes of ampicillin derived Schiffbase ligand and Nicotinamide: Synthesis, physico-chemical studies, DFT calculation, antibacterial study and molecular docking analysis
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A novel series of mixed-ligand complexes of the type, [ML 1 (L 2 ) 3 ]Cl x [M = Cr(III), Fe(III), Co(II),Ni(II), Cu(II), Cd(II) and Hg(II), n = 2, 3], was synthesized using Schiffbase (HL 1 ) as main ligand, nicotinamide (L 2 ) as secondary ligand, and the corresponding metal ions in 1:3:1 molar ratio. The main ligand, HL 1 was prepared by the interaction of ampicillin drug and 4-chlorobenzophenone. The synthesized mixed ligand complexes were characterized by elemental analysis, UV-Vis, FT-IR, 1 H-NMR, 13 C-NMR and TG/DTG studies. In the mixed-ligand complexes, the Schiffbase ligand, HL 1 showed coordination to the central metal ion in tridentate manner via azomethine nitrogen, β-lactam ring oxygen and deprotonated carboxylic oxy- gen atom

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Publication Date
Sun Mar 17 2019
Journal Name
Baghdad Science Journal
The Potential of some Plant Extracts as Radical Scavengers and Dipeptidyl Peptidase-4 Inhibitors
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Seeds, beans, leaves, fruit peel and seeds of five plants (Ferula assa-foetida, Coffea robusta, Olea europaea, Punica granatum and Vitis vinifera, respectively) were extracted with four solvents (distilled water, 80% methanol, 80% acetone and a mixed solvent that included methanol, ethanol, acetone and n-butanol at proportions 7:1:1:1). Such manipulation yielded 20 extracts, which were phytochemically analyzed for total polyphenols (TP) and flavonoids (TF). The DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging activity (RSA) and DPP-4 (dipeptidyl peptidase-4) relative inhibition activity (RIA) were also assessed for each extract. The results revealed that mixed solvent extract of V.

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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
Wed Oct 02 2024
Journal Name
International Development Planning Review
A COMPARATIVE STUDY OF THE AMOUNT OF FORCE EXERTED ON THE GROUND AND THE TIME OF PROPULSION IN THE VERTICAL AND HORIZONTAL JUMPING TESTS FROM STABILITY USING A FOOT SCAN DEVICE
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Publication Date
Fri Aug 01 2008
Journal Name
2008 First International Conference On The Applications Of Digital Information And Web Technologies (icadiwt)
Hybrid canonical genetic algorithm and steepest descent algorithm for optimizing likelihood estimators of ARMA (1, 1) model
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This paper presents a hybrid genetic algorithm (hGA) for optimizing the maximum likelihood function ln(L(phi(1),theta(1)))of the mixed model ARMA(1,1). The presented hybrid genetic algorithm (hGA) couples two processes: the canonical genetic algorithm (cGA) composed of three main steps: selection, local recombination and mutation, with the local search algorithm represent by steepest descent algorithm (sDA) which is defined by three basic parameters: frequency, probability, and number of local search iterations. The experimental design is based on simulating the cGA, hGA, and sDA algorithms with different values of model parameters, and sample size(n). The study contains comparison among these algorithms depending on MSE value. One can conc

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