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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 Aug 01 2023
Journal Name
Baghdad Science Journal
Performance Evaluation of a Triple Concentric Tube Heat Exchanger Using Deionized Water and Oil-40
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This study examines experimentally the performance of a horizontal triple concentric tube heat exchanger TCTHE made of copper metal using water as cooling fluid and oil-40 as hot fluid. Hot fluid enters the inner annular tube of the TCTHE in a direction at a temperature of 50, 60 and 70 oC and a flow rate of 20 l/hr. On the other hand, the cooling fluid enters the inner tube and the outer annular tube in the reverse direction (counter current flow) at a temperature of 25 oC and flow rates of 10, 15, 20, 25, 30 and 35 l/hr. The TCTHE is composed of three copper tubes with outer diameters of 34.925 mm, 22.25 mm, and 9.525 mm, and thicknesses of 1.27 mm, 1.143 mm, and 0.762 mm, respectively. TCTHE tube's length was 670

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Publication Date
Sat Apr 30 2022
Journal Name
Eastern-european Journal Of Enterprise Technologies
Improvement of noisy images filtered by bilateral process using a multi-scale context aggregation network
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Deep learning has recently received a lot of attention as a feasible solution to a variety of artificial intelligence difficulties. Convolutional neural networks (CNNs) outperform other deep learning architectures in the application of object identification and recognition when compared to other machine learning methods. Speech recognition, pattern analysis, and image identification, all benefit from deep neural networks. When performing image operations on noisy images, such as fog removal or low light enhancement, image processing methods such as filtering or image enhancement are required. The study shows the effect of using Multi-scale deep learning Context Aggregation Network CAN on Bilateral Filtering Approximation (BFA) for d

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Publication Date
Tue Jun 01 2021
Journal Name
Iop Conference Series: Earth And Environmental Science
Treatment of Al-Muthanna Petroleum Refinery Wastewater by Electrocoagulation Using a Tubular batch Electrochemical Reactor
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Abstract<p>An electrocoagulation process has been used to eliminate the chemical oxygen demand (COD) from wastewaters discharged from the Al-Muthanna petroleum refinery plant. In this process, a circular aluminum bar was used as a sacrificial anode, and hallow cylinder made from stainless steel was used as a cathode in a tubular batch electrochemical Reactor. Impacts of the operating factors like current density (5-25mAcm<sup>-2</sup>), NaCl addition at concentrations (0-2g/l), and pH at values (3-11) on the COD removal efficiency were studied.</p><p>Results revealed that the increase in current density increases the COD removal efficiency, whereas an increase</p> ... Show More
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Publication Date
Thu Jun 10 2010
Journal Name
Iraqi Journal Of Laser
Experimental Investigation of a Laser Wireless Video Communication System Using Intensity Modulated /Direct Detection Technique
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In this work Laser wireless video communication system using intensity modualtion direct
detection IM/DD over a 1 km range between transmitter and receiver is experimentally investigated and
demonstrated. Beam expander and beam collimeter were implemented to collimete laser beam at the
transmitter and focus this beam at the receiver respectively. The results show that IM/DD communication
sysatem using laser diode is quite attractive for transmitting video signal. In this work signal to noise
ratio (S/N) higher than 20 dB is achieved in this work.

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Publication Date
Mon Jun 01 2015
Journal Name
Conference: 8th International Conference And Exhibition On Design And Production Of Machines And Dies/molds
Design, Construction, and Controlling of A Shaped Metal Deposition Machine Using Arc Metal-Wire System
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Publication Date
Thu Aug 01 2019
Journal Name
مجلة العلوم الاقتصادية والإدارية
Improving" Jackknife Instrumental Variable Estimation method" using A class of immun algorithm with practical application
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Improving" Jackknife Instrumental Variable Estimation method" using A class of immun algorithm with practical application

Publication Date
Fri Jan 01 2021
Journal Name
Journal Of Engineering
A Computational Fluid Dynamics Investigation of using Large-Scale Geometric Roughness Elements in Open Channels
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The hydraulic behavior of the flow can be changed by using large-scale geometric roughness elements in open channels. This change can help in controlling erosions and sedimentations along the mainstream of the channel. Roughness elements can be large stone or concrete blocks placed at the channel's bed to impose more resistance in the bed. The geometry of the roughness elements, numbers used, and configuration are parameters that can affect the flow's hydraulic characteristics. In this paper, velocity distribution along the flume was theoretically investigated using a series of tests of T-shape roughness elements, fixed height, arranged in three different configurations, differ in the number of lines of roughness element

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Publication Date
Tue Oct 26 2021
Journal Name
Series On Biomechanics
Monitoring and analysis of plantar pressure map and foot motions using a wearable sensing system
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Publication Date
Mon Aug 01 2016
Journal Name
Journal Of Engineering
Prediction of Monthly Fluoride Content in Tigris River using SARIMA Model in R Software
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The need to create the optimal water quality management process has motivated researchers to pursue prediction modeling development. One of the widely important forecasting models is the sessional autoregressive integrated moving average (SARIMA) model. In the present study, a SARIMA model was developed in R software to fit a time series data of monthly fluoride content collected from six stations on Tigris River for the period from 2004 to 2014. The adequate SARIMA model that has the least Akaike's information criterion (AIC) and mean squared error (MSE) was found to be SARIMA (2,0,0) (0,1,1). The model parameters were identified and diagnosed to derive the forecasting equations at each selected location. The correlation coefficien

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Publication Date
Mon Oct 22 2018
Journal Name
Journal Of Economics And Administrative Sciences
Using Mehar method to change fuzzy cost of fuzzy linear model with practical application
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  Many production companies suffers from big losses because of  high production cost and low profits for several reasons, including raw materials high prices and no taxes impose on imported goods also consumer protection law deactivation and national product and customs law, so most of consumers buy imported goods because it is characterized by modern specifications and low prices.

  The production company also suffers from uncertainty in the cost, volume of production, sales, and availability of raw materials and workers number because they vary according to the seasons of the year.

  I had adopted in this research fuzzy linear program model with fuzzy figures

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