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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 01 2024
Journal Name
Journal Of Engineering
Face-based Gender Classification Using Deep Learning Model
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Gender classification is a critical task in computer vision. This task holds substantial importance in various domains, including surveillance, marketing, and human-computer interaction. In this work, the face gender classification model proposed consists of three main phases: the first phase involves applying the Viola-Jones algorithm to detect facial images, which includes four steps: 1) Haar-like features, 2) Integral Image, 3) Adaboost Learning, and 4) Cascade Classifier. In the second phase, four pre-processing operations are employed, namely cropping, resizing, converting the image from(RGB) Color Space to (LAB) color space, and enhancing the images using (HE, CLAHE). The final phase involves utilizing Transfer lea

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Publication Date
Tue Oct 19 2021
Journal Name
International Journal Of Online And Biomedical Engineering (ijoe)
Object Tracking Using Adaptive Diffusion Flow Active Model
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Object tracking is one of the most important topics in the fields of image processing and computer vision. Object tracking is the process of finding interesting moving objects and following them from frame to frame. In this research, Active models–based object tracking algorithm is introduced. Active models are curves placed in an image domain and can evolve to segment the object of interest. Adaptive Diffusion Flow Active Model (ADFAM) is one the most famous types of Active Models. It overcomes the drawbacks of all previous versions of the Active Models specially the leakage problem, noise sensitivity, and long narrow hols or concavities. The ADFAM is well known for its very good capabilities in the segmentation process. In this

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Publication Date
Thu Jan 21 2021
Journal Name
Recent Innovations In Chemical Engineering (formerly Recent Patents On Chemical Engineering)
Soap Production Using Vacuum Reactive Distillation: Batch Model
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Introduction: Although soap industry is known from hundreds of years, the development accompanied with this industry was little. The development implied the mechanical equipment and the additive materials necessary to produce soap with the best specifications of shape, physical and chemical properties. Objectives: This research studies the use of vacuum reactive distillation VRD technique for soap production. Methods: Olein and Palmitin in the ratio of 3 to 1 were mixed in a flask with NaOH solution in stoichiometric amount under different vacuum pressures from -0.35 to -0.5 bar. Total conversion was reached by using the VRD technique. The soap produced by the VRD method was compared with soap prepared by the reaction - only method which

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Publication Date
Sat Oct 01 2022
Journal Name
Baghdad Science Journal
COVID-19 Diagnosis System using SimpNet Deep Model
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After the outbreak of COVID-19, immediately it converted from epidemic to pandemic. Radiologic images of CT and X-ray have been widely used to detect COVID-19 disease through observing infrahilar opacity in the lungs. Deep learning has gained popularity in diagnosing many health diseases including COVID-19 and its rapid spreading necessitates the adoption of deep learning in identifying COVID-19 cases. In this study, a deep learning model, based on some principles has been proposed for automatic detection of COVID-19 from X-ray images. The SimpNet architecture has been adopted in our study and trained with X-ray images. The model was evaluated on both binary (COVID-19 and No-findings) classification and multi-class (COVID-19, No-findings

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Publication Date
Wed Mar 30 2022
Journal Name
Journal Of Economics And Administrative Sciences
Euro Dinar Trading Analysis Using WARIMA Hybrid Model
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The rise in the general level of prices in Iraq makes the local commodity less able to compete with other commodities, which leads to an increase in the amount of imports and a decrease in the amount of exports, since it raises demand for foreign currencies while decreasing demand for the local currency, which leads to a decrease in the exchange rate of the local currency in exchange for an increase in the exchange rate of currencies. This is one of the most important factors affecting the determination of the exchange rate and its fluctuations. This research deals with the currency of the European Euro and its impact against the Iraqi dinar. To make an accurate prediction for any process, modern methods can be used through which

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Publication Date
Sun Nov 01 2020
Journal Name
Journal Of Engineering
Agile manufacturing assessment model using multi-grade evaluation
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In unpredicted industrial environment, being able to adapt quickly and effectively to the changing is key in gaining a competitive advantage in the global market. Agile manufacturing evolves new ways of running factories to react quickly and effectively to changing markets, driven by customized requirement. Agility in manufacturing can be successfully achieved via integration of information system, people, technologies, and business processes. This article presents the conceptual model of agility in three dimensions named: driving factor, enabling technologies and evaluation of agility in manufacturing system. The conceptual model was developed based on a review of the literature. Then, the paper demonstrates the agility

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Publication Date
Thu Dec 01 2016
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
THE OCCURRENCE OF THREE MONOGENEAN PARASITE SPECIES FOR THE FIRST TIME IN IRAQ ON GILLS OF THE COMMON CARP CYPRINUS CARPIO LINNAEUS, 1758 (CYPRINIFORMES, CYPRINIDAE)
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    The monogeneans Gyrodactylus dzhalilovi Ergens & Ashurova, 1984, G. magnus Konovalov, 1967 and G. matovi Ergens & Kakachava-Avramova, 1966 were recorded in this study for the first time in Iraq from gills of the common carp Cyprinus carpio Linnaeus, 1758 collected from Tigris River in Baghdad city. The description, measurements and illustrations of these parasites were given.

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Publication Date
Sat Jul 30 2022
Journal Name
Global Academic Journal Of Linguistics And Literature
A Critical Stylistic Analysis of Transcultural Identity in Lyer’s The Global Soul (2001) Using the Tool of Negation
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This study is intended to examine the concept of transcultural identity in the travel book The Global Soul: Jet Lag, Shopping Malls, and the Search for Home by (Iyer, 2001). Jeffries’ model of critical stylistics (2010) (henceforth, CS) has been selected to analyze the book. To be more specific, Negation is selected to analyze the concept under study. As such, the study aims at finding out how Negation is used to portray ideological meanings representing the concept of transcultural identity in one non-fictional travel book; and finding out the ideologies related to the concept analyzed. The analysis of the data shows that Negation is a suitable analytical tool to reach the ideational meaning of the text towards the concept of tra

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Publication Date
Thu Apr 30 2020
Journal Name
Journal Of Economics And Administrative Sciences
Rainwater Drainage Service Improvement Using a Number Of Quality Tools at the Directorate of Karbala Sewage
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The basic objective of the research is to study the quality of the water flow service in the Directorate of Karbala sewage and how to improve it after identifying the deviations of the processes and the final product and then providing the possible solutions in addressing the causes of the deviations and the associated quality gaps. A number of quality tools were used and applied to all data Stations with areas and activities related to the drainage of rainwater, as the research community determines the stations of lifting rainwater in the Directorate of the streams of Karbala holy, and the station was chosen Western station to apply the non-random sampling method intended after meeting a number of. It is one of the largest and m

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Publication Date
Sat Aug 01 2020
Journal Name
Journal Of Engineering Science And Technology (jestec)
Influence of A River Water Quality on The Efficiency of Water Treatment Using Artificial Neural Network
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Tigris River is the lifeline that supplies a great part of Iraq with water from north to south. Throughout its entire length, the river is battered by various types of pollutants such as wastewater effluents from municipal, industrial, agricultural activities, and others. Hence, the water quality assessment of the Tigris River is crucial in ensuring that appropriate and adequate measures are taken to save the river from as much pollution as possible. In this study, six water treatment plants (WTPs) situated on the two-banks of the Tigris within Baghdad City were Al Karkh; Sharq Dijla; Al Wathba; Al Karama; Al Doura, and Al Wahda from northern Baghdad to its south, that selected to determine the removal efficiency of turbidity and

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