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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 May 01 2021
Journal Name
Journal Of Physics: Conference Series
The classification of fetus gender based on fuzzy C-mean using a hybrid filter
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This paper proposes a new approach, of Clustering Ultrasound images using the Hybrid Filter (CUHF) to determine the gender of the fetus in the early stages. The possible advantage of CUHF, a better result can be achieved when fuzzy c-mean FCM returns incorrect clusters. The proposed approach is conducted in two steps. Firstly, a preprocessing step to decrease the noise presented in ultrasound images by applying the filters: Local Binary Pattern (LBP), median, median and discrete wavelet (DWT),(median, DWT & LBP) and (median & Laplacian) ML. Secondly, implementing Fuzzy C-Mean (FCM) for clustering the resulted images from the first step. Amongst those filters, Median & Laplace has recorded a better accuracy. Our experimental evaluation on re

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Publication Date
Sun Jun 01 2014
Journal Name
Baghdad Science Journal
Comparative study of hydatid cysts isolated from livers of different hosts
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Fifty three hydatid cysts were collected from different hosts, sheep, goats and cattle , from many slaughterhouse in Salahadin and Baghdad , while human's hydatid cysts samples were collected from Tikrit educational hospital and Tofiqe civilian hospital patients . The study included a biochemical comparison of some hydatid cyst fluid criteria such as, glucose, total protein, pH, glutamate pyrovate transaminase enzyme (GPT) , glutamate oxaloacetate transaminase enzyme (GOT) , acid phosphatase (ACP) , Alkaline Phosphatase (ALP) , and also studied protoscolices viability,the current study showed the differences in chemical composition of hydatid cyst fluids back to host type and parasite strain .

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Publication Date
Wed Apr 01 2015
Journal Name
Journal Of Environmental Engineering
Using Granular Dead Anaerobic Sludge as Permeable Reactive Barrier for Remediation of Groundwater Contaminated with Phenol
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Publication Date
Sat Aug 01 2020
Journal Name
Journal Of Water Process Engineering
Humic acid coated sand as a novel sorbent in permeable reactive barrier for environmental remediation of groundwater polluted with copper and cadmium ions
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Plantation of humic acid nanoparticles on the inert sand through simple impregnation to obtain the permeable reactive barrier (PRB) for treating of groundwater contaminated with copper and cadmium ions. The humic acid was extracted from sewage sludge which is byproduct of the wastewater treatment plant; so, this considers an application of sustainable development. Batch tests signified that the coated sand by humic acid (CSHA) had removal efficiencies exceeded 98 % at contact time, sorbent dosage, and initial pH of 1 h, 0.25 g/50 mL and 7, respectively for 10 mg/L initial concentration and 200 rpm agitation speed. Results proved that physicosorption was the predominant mechanism for metals-CSHA interaction because the sorption data followed

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Publication Date
Sun Dec 15 2019
Journal Name
Al-academy
Directorial Vision and its Relation to Scenographic Proposal in the Iraqi Theater Show- The Play of Darkness -A Model: رامي سامح زكي
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The increase of the scenographic designer role on account of the character of the director in the Iraqi theater constituted a clear phenomenon that has been manifested in many shows, which necessitated a stance on the nature of this relation and delimiting the work space for each one of them inside the theater show. The research focuses on determining the work relation between the directorial vision and the scenographic proposal in the Iraq theater show. The research is divided into four chapters, the first one addressed the methodological framework, where the research problem was stated in the following question (has the scenographic designer been able through his scenographic proposal to remove the director from his position being the

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Publication Date
Mon Sep 01 2025
Journal Name
Thermal Science And Engineering Progress
Active mixing strategies for energy-efficient water dispensers: Comparative experimental study of impeller and bubble injection in hot climates
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Publication Date
Thu Mar 15 2018
Journal Name
Arab World English Journal
Pedagogical Stylistics as a Tool in the Classroom: An Investigation of EFL Undergraduate Students' Ability in Analyzing Poetic Language
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Publication Date
Mon Jan 01 2018
Journal Name
Journal Of Wildlife Diseases
MENINGEAL WORM (PARELAPHOSTRONGYLUS TENUIS) AS A CAUSE OF MORTALITY IN THE RESTORED ELK (CERVUS CANADENSIS) POPULATION IN MISSOURI, USA
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Publication Date
Thu Mar 01 2018
Journal Name
Arab World English Journal
Pedagogical Stylistics as a Tool in the Classroom: An Investigation of EFL Undergraduate Students' Ability in Analyzing Poetic Language
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Publication Date
Wed Jan 30 2019
Journal Name
Journal Of The College Of Education For Women
The Impact of Applying Mind Mapping Technique as a Pre- Writing Tool on EFL College Students in Essay Writing
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Based on the assumption that the more teachers know about brain science, the better
prepared they will be to make instructional decisions.
Mind Mapping is a powerful tool for assisting any form of writing. Language is an
important device and a very beneficial means for human being to communicate with other
people .Writing is one of the language skills that will never be left in education.
The study aims at investigating the Impact of applying mind mapping technique as a prewriting
tool on Iraqi EFL college students in essay writing. To do so, 60 EFL college students
were divided randomly selected and divided into two groups experimental and control. Prior
to treatment, participants of the both groups were given a

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