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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 Jan 02 2017
Journal Name
Al-academy
How to build a virtual personal imagined in the picture, directed by James Cameron (Avatar) movie as a model
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The personal drama in particular, and one of the key elements underlying the dramatic structure to convey ideas and visions presented by the author when writing the text of the dramatic fall after that on the way out the submission form that suits the proposals of the text and processors directorial would push the wheel of dramatic structure to the front. So take the maker of the artwork (writer) undertook the transfer of those events and personalities in art presumed sometimes real and sometimes, in order to enrich the art inspired by the human reality through the ages, and full of its themes and ideas that led to the development experiences of peoples experiences of living. Therefore, we find it important to research in the characters

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Publication Date
Sun Apr 01 2018
Journal Name
Journal Of Economics And Administrative Sciences
Designing and Application of Mathematical Model A Multi – Objectives for Assessment The Quality Of The Project : A Case Study at Saad Public Construction Company
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Abstract

This research aims to design a multi-objective mathematical model to assess the project quality based on three criteria: time, cost and performance. This model has been applied in one of the major projects formations of the Saad Public Company which enables to completion the project on time at an additional cost that would be within the estimated budget with a satisfactory level of the performance which match with consumer requirements. The problem of research is to ensure that the project is completed with the required quality Is subject to constraints, such as time, cost and performance, so this requires prioritizing multiple goals. The project

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Publication Date
Mon Sep 20 2021
Journal Name
Journal Of Craniofacial Surgery
Presurgical Assessment of Anatomical Landmark Position Using Two Views of Cone Beam Computed Tomography: A Comparative Radiological Study
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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 Sep 30 2015
Journal Name
College Of Islamic Sciences
The other day in the Holy Quran and the four Gospels: A comparative study
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The other day in the Holy Quran and the four Gospels

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Publication Date
Thu Apr 01 2021
Journal Name
Journal Of Molecular Structure
Mixed-ligand complexes of ampicillin derived Schiff base 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, [ML1(L2)3]Clx [M= Cr(III), Fe(III), Co(II),Ni(II), Cu(II), Cd(II) and Hg(II), n = 2, 3], was synthesized using Schiff base (HL1) as main ligand, nicotinamide (L2) as secondary ligand, and the corresponding metal ions in 1:3:1 molar ratio. The main ligand, HL1 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,1H-NMR,13C-NMR and TG/DTG studies. In the mixed-ligand complexes, the Schiff base ligand, HL1 showed coordination to the central metal ion in tridentate manner via azomethine nitrogen, β-lactam ring oxygen and deprotonated carboxylic oxygen atoms, whereas the sec

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Publication Date
Mon May 30 2022
Journal Name
Egyptian Journal Of Chemistry
Design ,Synthesis, Insilco Study and Biological Evaluation of New Coumarin-Oxadiazole Derivatives as Potent Histone Deacetylase Inhibitors
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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
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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