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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
Thu Jan 01 2009
Journal Name
Journal Of The College Of Languages (jcl)
Graphic Novels : A Privilege For Teachers and Students
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There are many ways to communicate a story, one can tell it, sing it, act it, write it, film it and can draw it. Each form of storytelling has its unique characteristics that separate it from the other forms. These distinguishing characteristics of each form does not indicate the superiority of one form over the other, on the contrary, it indicates the human ability to be creative on many levels. As students of literature, only the written form of a story is taken into account. One reason for the negligence of other forms of storytelling might be that singing and filming a story is not related to literature. But there has been a form of storytelling that uses words along with pictures which eventually became a genre of novels called grap

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Publication Date
Mon Apr 17 2023
Journal Name
Wireless Communications And Mobile Computing
A Double Clustering Approach for Color Image Segmentation
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One of the significant stages in computer vision is image segmentation which is fundamental for different applications, for example, robot control and military target recognition, as well as image analysis of remote sensing applications. Studies have dealt with the process of improving the classification of all types of data, whether text or audio or images, one of the latest studies in which researchers have worked to build a simple, effective, and high-accuracy model capable of classifying emotions from speech data, while several studies dealt with improving textual grouping. In this study, we seek to improve the classification of image division using a novel approach depending on two methods used to segment the images. The first

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Publication Date
Mon Nov 21 2022
Journal Name
Coatings
Nondestructive Testing Technologies for Rail Inspection: A Review
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Alongside the development of high-speed rail, rail flaw detection is of great importance to ensure railway safety, especially for improving the speed and load of the train. Several conventional inspection methods such as visual, acoustic, and electromagnetic inspection have been introduced in the past. However, these methods have several challenges in terms of detection speed and accuracy. Combined inspection methods have emerged as a promising approach to overcome these limitations. Nondestructive testing (NDT) techniques in conjunction with artificial intelligence approaches have tremendous potential and viability because it is highly possible to improve the detection accuracy which has been proven in various conventional nondestr

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Publication Date
Mon Jun 05 2023
Journal Name
Journal Of Engineering
A Computerized Integrated System for Geodetic Networks Design
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This research presents a model for surveying networks configuration which is designed and called a Computerized Integrated System for Triangulation Network Modeling (CISTNM). It focuses on the strength of figure as a concept then on estimating the relative error (RE) for the computed side (base line) triangulation element. The CISTNM can compute the maximum elevations of the highest
obstacles of the line of sight, the observational signal tower height, the contribution of each triangulation station with their intervisibility test and analysis. The model is characterized by the flexibility to select either a single figure or a combined figures network option. Each option includes three other implicit options such as: triangles, quadri

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Publication Date
Thu Feb 01 2024
Journal Name
Bulletin Of Electrical Engineering And Informatics
A systematic literature review for smart hydroponic system
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Hydroponics is the cultivation of plants by utilizing water without using soil which emphasizes the fulfillment of the nutritional needs of plants. This research has introduced smart hydroponic system that enables regular monitoring of every aspect to maintain the pH values, water, temperature, and soil. Nevertheless, there is a lack of knowledge that can systematically represent the current research. The proposed study suggests a systematic literature review of smart hydroponics system to overcome this limitation. This systematic literature review will assist practitioners draw on existing literature and propose new solutions based on available knowledge in the smart hydroponic system. The outcomes of this paper can assist future r

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Publication Date
Sun Jul 01 1990
Journal Name
Bulletin Of The Iraq Natural History Museum (p-issn: 1017-8678 , E-issn: 2311-9799)
KEY TO THE SPECIES OF THE GENUS STACHYS L. (LABIATAE) IN IRAQ WITH THREE NEW RECORDS
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A simplified parallel key was presented in this work for the Taxa of Stackys L. wildly grown in Iraq. Three records within this genus were newly recorded to our country in the present work and they are S. kermanshahansis Rech S. setifera C.A. Mey. subsp setifera, S. setifera ssp iranica (Reck.) The characteristics of these new records were also given with some representative specimens.

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Publication Date
Wed Nov 21 2018
Journal Name
International Journal Of Control, Automation And Systems
Design and Stability Analysis of a Fractional Order State Feedback Controller for Trajectory Tracking of a Differential Drive Robot
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Publication Date
Fri Jan 01 2021
Journal Name
Chemical Science
Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step
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Fluorescent proteins (FPs) have revolutionised the life sciences, but the chromophore maturation mechanism is still not fully understood. Here we photochemically trap maturation at a crucial stage and structurally characterise the intermediate.

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Publication Date
Sun Jun 01 2025
Journal Name
Results In Materials
Adsorption, thermodynamic and corrosion study of enalapril malate pharmaceutical drug as corrosion inhibitor for carbon steel in saline solution
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Unused and expired pharmaceutical drugs are a novel type of organic corrosion inhibitor. They are less expensive, more effective, and less harmful than conventional organic corrosion inhibitors. This study investigated the effects of concentration, adsorption mechanism and thermodynamic parameters of enalapril malate (ENAP) as a corrosion inhibitor for carbon steel in a saline solution (3.5 % NaCl). The polarization method was used to determine the corrosion rate and inhibition efficiency. Field emission scanning electron microscopy (FE-SEM) and atomic force spectroscopy (AFM) were used to investigate the surface morphology and topography of carbon steel after immersion in both uninhibited and inhibited media for 24 h. Fourier transform inf

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Publication Date
Sat Jan 25 2025
Journal Name
Al-mansour Journal
The Multi-Period Probabilistic Inventory Model Applied at the General Company for Leather Industries
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In this research, the multi-period probabilistic inventory model will be applied to the stores of raw materials used in the leather industry at the General Company for Leather Industries. The raw materials are:Natural leather includes cowhide, whether imported or local, buffalo leather, lamb leather, goat skin, chamois (raw materials made from natural leather), polished leather (raw materials made from natural leather), artificial leather (skai), supplements which include: (cuffs - Clocks - hands - pockets), and threads.This model was built after testing and determining the distribution of demand during the supply period (waiting period) for each material and completely independently from the rest of the materials, as none of the above mate

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