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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
Tue Nov 19 2019
Journal Name
Iranian Journal Of Science And Technology, Transactions A: Science
Systematic Study of the Nuclear Structure for Some Exotic Nuclei Using Skyrme–Hartree–Fock Method
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The ground state charge, neutron, proton and matter densities, the associated nuclear radii and the binding energy per nucleon of 8B, 17Ne, 23Al and 27P halo nuclei have been investigated using the Skyrme–Hartree–Fock (SHF) model with the new SKxs25 parameters. According to the calculated results, it is found that the SHF model with these Skyrme parameters provides a good description on the nuclear structure of above proton-rich halo nuclei. The elastic charge form factors of 8B and 17Ne halo nuclei and those of their stable isotopes 10B and 20Ne are calculated using plane-wave Born approximation with the charge density distributions obtained by SHF model to investigate the effect of the extended charge distributions of proton-rich nucl

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Publication Date
Sun Jun 20 2021
Journal Name
Baghdad Science Journal
A Word Cloud Model based on Hate Speech in an Online Social Media Environment
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Social media is known as detectors platform that are used to measure the activities of the users in the real world. However, the huge and unfiltered feed of messages posted on social media trigger social warnings, particularly when these messages contain hate speech towards specific individual or community. The negative effect of these messages on individuals or the society at large is of great concern to governments and non-governmental organizations. Word clouds provide a simple and efficient means of visually transferring the most common words from text documents. This research aims to develop a word cloud model based on hateful words on online social media environment such as Google News. Several steps are involved including data acq

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Publication Date
Thu Feb 01 2024
Journal Name
Baghdad Science Journal
Building a Sustainable GARCH Model to Forecast Rubber Price: Modified Huber Weighting Function Approach
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The unstable and uncertain nature of natural rubber prices makes them highly volatile and prone to outliers, which can have a significant impact on both modeling and forecasting. To tackle this issue, the author recommends a hybrid model that combines the autoregressive (AR) and Generalized Autoregressive Conditional Heteroscedasticity (GARCH) models. The model utilizes the Huber weighting function to ensure the forecast value of rubber prices remains sustainable even in the presence of outliers. The study aims to develop a sustainable model and forecast daily prices for a 12-day period by analyzing 2683 daily price data from Standard Malaysian Rubber Grade 20 (SMR 20) in Malaysia. The analysis incorporates two dispersion measurements (I

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Publication Date
Tue Feb 18 2025
Journal Name
Iranian Journal Of Science
Exploring Neimark-Sacker Bifurcation and Chaos Control in a Tri-species Discrete-Time Model
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Publication Date
Sun Jul 09 2023
Journal Name
Journal Of Engineering
A study of the Effect of Air Inlet and Exit on Indoor Air Movement
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This work consists of a numerical simulation to predict the velocity and temperature distributions, and an experimental work to visualize the air flow in a room model. The numerical work is based on non-isothermal, incompressible, three dimensional, k turbulence model, and solved using a computational fluid dynamic (CFD) approach, involving finite volume technique to solve continuity, momentum and energy equations, that governs the room’s turbulent flow domain. The experimental study was performed using (1/5) scaled room model of the actual dimensions of the room to simulate room air flow and visualize the flow pattern using smoke generated  from burnt herbs and collected in a smoke generator to delivered through

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Publication Date
Wed Dec 15 2021
Journal Name
Al-academy
Realism in the painting of Iraqi Kurdistan artists "A Study in methods of expression"
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The tagged research (realism in the Paintings of Iraqi Kurdistan artists, “a study of expression methods”) dealt with realism in an objective way, as well as the complexity of its concepts through its formations and formations. On realism and its historical dimension in concept and meaning, as for the second chapter, the research was focused on the methods of expression in painting, while the third chapter was concerned with the procedural applications of realistic methods of expression in the drawings of Iraqi Kurdistan, and according to these axes and to achieve the goal of the research, a number of Among the results are:
1- Realism documented the life of the Kurdish society in line with the developments of the era, as the sty

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Publication Date
Wed May 31 2017
Journal Name
Journal Of Engineering
A Study of Parameters Affecting the Solvent Extraction-Flocculation Process of Used Lubricating Oil
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The aim of this study was to investigate the effect of operating variables on, the percentage of removed sludge (PSR) obtained during re-refining of 15W-40 Al-Durra spent lubricant by solvent extraction-flocculation treatment method. Binary solvents were used such as, Heavy Naphtha (H.N.): MEK (N:MEK), H.N. : n-Butanol (N:n-But), and H.N. : Iso-Butanol (N:Iso:But). The studied variables were mixing speed (300-900, rpm), mixing time (15-60, min), and operating  temperature (2540, oC). This study showed that the studied operating variables have effects where, increasing the mixing time up to 45 min for H.N.: MEK, H.N.: n-Butanol  and 30 min for H.N.: Iso-Butanol increased the PSR, after that percentage was decreased; increasing t

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Publication Date
Tue Feb 12 2019
Journal Name
Iraqi Journal Of Physics
A study of the structural and electrical properties of Ni1-x Cox Fe2O4 ferrites
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Ferrite with general formula Ni1-x Cox Fe2O4(where x=0.0.1,0.3,0.5,0.7, and 0.9), were prepared by standard ceramic technique. The main cubic spinel structure phase for all samples was confirmed by x-ray diffraction patterns. The lattice parameter results were (8.256-8.299 °A). Generally, x -ray density increased with the addition of Cobalt and showed value between (5.452-5.538gm/cm3). Atomic Force Microscopy (AFM) showed that the average grain size and surface roughness was decreasing with the increasing cobalt concentration. Scanning Electron Microscopy images show that grains had an irregular distribution and irregular shape. The A.C conductivity was found to increase with the frequency and the addition of Cobal

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Publication Date
Sat Oct 01 2011
Journal Name
Iraqi Journal Of Physics
A Study of the mechanical properties of aluminum composite materials prepared by atomization process
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Steel fiber aluminum matrix composites were prepared by atomization technique. Different air atomization conditions were considered; which were atomization pressure and distance between sample and nozzle. Tensile stress properties were studied. XRF and XRD techniques were used to study the primary compositions and the structure of the raw materials and the atomized products. The tensile results showed that the best reported tensile strength observed for an atomization pressure equal to 4 mbar and sample to nozzle distance equal to 12 cm. Young modulus results showed that the best result occurred with an air atomization pressure equal to 8 mbar and sample to nozzle distance equal to 16cm

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Publication Date
Wed Aug 31 2022
Journal Name
Mathematical Modelling Of Engineering Problems
Evaluation of Al-Ishaqi Irrigation Project: A Case Study Eastern Canal of the Project
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An evaluation the performance of the irrigation system for the Al-Ishaqi irrigation project for the Eastern Canal was conducted to identify management strategies that can be used to improve the operation and performance of the irrigation system. The study area is located in Salah al-Din G.0overnorate, Iraq. The field work included determining the moisture content of the soil before and after irrigation, measuring the inflow of the field to find the depth of the applied water, field monitoring, and measuring the depth of the root zone for each irrigation process. Field measurements showed that the average efficiency of water application for the two fields (A, and B) are 59.81% and 38.6%, respectively. The results of the efficiency of

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