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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 Jul 11 2022
Journal Name
Aip Conference Proceedings
Well placement optimization: A review
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Optimization of well placement plays a considerable role in the production and maximizing the net present value of the investment of oil field developments. However, the application of the optimization techniques in well placement developments is so complicated because many decision variables, objective functions, and constraints are involved in the well placement optimization case. Furthermore, many computational techniques; conventional and non-conventional, have been utilized to optimize well placement operations. This study displays the advancement of the optimization methods applied in the well placement. Subsequently, the study assorted the applied optimization methods, and it demonstrates the restriction and the range of implementati

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Publication Date
Wed Jan 01 2025
Journal Name
Journal Of Computer Sciences And Informatics
Edge Detection Methods: A Review
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This article studies a comprehensive methods of edge detection and algorithms in digital images which is reflected a basic process in the field of image processing and analysis. The purpose of edge detection technique is discovering the borders that distinct diverse areas of an image, which donates to refining the understanding of the image contents and extracting structural information. The article starts by clarifying the idea of an edge and its importance in image analysis and studying the most noticeable edge detection methods utilized in this field, (e.g. Sobel, Prewitt, and Canny filters), besides other schemes based on distinguishing unexpected modifications in light intensity and color gradation. The research as well discuss

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Publication Date
Fri Jun 01 2012
Journal Name
Journal Of The College Of Languages (jcl)
Meaning From a Logical Perspective
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This paper is intended to focus on the existing relation between 'logic' and 'meaning', and how 'meaning' is looked at through logical perspective. Besides, this paper adopts simple logical symbols to represent some aspects of meaning.

    Since meaning is still regarded as a thorny area that needs further study to determine its nature and borderline, this paper proposes to resort to logic and logical rules. This paper points out how logical rules are used and how they clarify some oblique sentences. The paper also sheds light on how meaningful sentences are logically symbolized and how logic can define the borderline of meaning in an adequate manner. This paper hypothesizes that logic, l

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Publication Date
Mon Aug 15 2022
Journal Name
Journal Of Al-qadisiyah For Computer Science And Mathematics
Passport Photo Compression: A Review
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The demand for electronic -passport photo ( frontal facial) images has grown rapidly. It now extends to Electronic Government (E-Gov) applications such as social benefits driver's license, e-passport, and e-visa . With the COVID 19 (coronavirus disease ), facial (formal) images are becoming more widely used and spreading quickly, and are being used to verify an individual's identity, but unfortunately that comes with insignificant details of constant background which leads to huge byte consumption that affects storage space and transmission, where the optimal solution that aims to curtail data size using compression techniques that based on exploiting image redundancy(s) efficiently.

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Publication Date
Mon Dec 01 2025
Journal Name
International Journal Of Science And Technology (ijst)
Cystic Echinococcosis: A Review Article
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Hydatid cystic or cystic echinococcosis disease remains a major challenge due to its medical and veterinary importance and its widespread spread all over the world as well as the economic losses caused by this disease, whether for humans or farm animals. Echinococcus granulosus is the causative agent for this disease, targeting the liver and lungs primarily and in varying proportions of the rest of the body. This disease is characterized by the non-appearance of pathological symptoms for long periods as its appearance depends on the size, number and site of the cysts formed and the type of organ infected and surgery is still the most effective solution for the disposal of hydatid cysts. Dogs and the rest of Canidae family represent the fina

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Publication Date
Wed Aug 30 2023
Journal Name
Iraqi Journal Of Science
Epidemiological Complex Networks: A Survey
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     In this review paper, several research studies were surveyed to assist future researchers to identify available techniques in the field of infectious disease modeling across complex networks. Infectious disease modelling is becoming increasingly important because of the microbes and viruses that threaten people’s lives and societies in all respects. It has long been a focus of research in many domains, including mathematical biology, physics, computer science, engineering, economics, and the social sciences, to properly represent and analyze spreading processes. This survey first presents a brief overview of previous literature and some graphs and equations to clarify the modeling in complex networks, the detection of soc

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Publication Date
Mon Jul 11 2022
Journal Name
Aip Conference Proceedings
Gas lift optimization: A review
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Optimization of gas lift plays a substantial role in production and maximizing the net present value of the investment of oil field projects. However, the application of the optimization techniques in gas lift project is so complex because many decision variables, objective functions and constraints are involved in the gas lift optimization problem. In addition, many computational ways; traditional and modern, have been employed to optimize gas lift processes. This research aims to present the developing of the optimization techniques applied in the gas lift. Accordingly, the research classifies the applied optimization techniques, and it presents the limitations and the range of applications of each one to get an acceptable level of accura

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Publication Date
Thu Dec 15 2022
Journal Name
Al-academy
Discourse the presence of animals in Mesopotamian sculptures "The lion and the bull as an example"
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Showing animal shapes is one of the primary topics since the discovery of cave drawings, with semantic discourses, as they appeared in the ancient civilization of Iraq, with their discourse and intellectual structure, and their reflections on their plastic achievements. The research deals with three topics: the first (an introduction to the concept of discourse), the second: (the historical roots of animal forms), and the third (the manifestation of animal forms and their discourse, in Mesopotamia). Mesopotamian fauna and its concepts? What are the?, Its importance was also represented in: the presence of animals and their semantic and conceptual discourse, especially the sculptures (the lion and the bull), with the aim of revealing the

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Publication Date
Tue Mar 15 2022
Journal Name
Al-academy
The culturalization of gender action in the Iraqi theatrical address the play " Revelations as an example"
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The culturalization of gender action occupies a wide range in culture, thoughts and modern studies as well as in fine arts and the ways of expressing them.

       Theater, as one of these arts, plays roles in establishing the fundamental concepts that aims at stating the uncontrollable deed of the social community. It remains one of the most effective and suitable means to confine the uncivilized practices to overcome a certain crisis after gender and cyborg in societies.

        The research concentrates on studying the culturalization of gender action in the Iraqi theatrical address because of the effect it has on the modernizing thought in arts and theater literature. It consists of chapter one which deals w

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Publication Date
Tue Sep 01 2020
Journal Name
Baghdad Science Journal
Reconstruction of Three-Dimensional Object from Two-Dimensional Images by Utilizing Distance Regularized Level Algorithm and Mesh Object Generation
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Three-dimensional (3D) reconstruction from images is a most beneficial method of object regeneration by using a photo-realistic way that can be used in many fields. For industrial fields, it can be used to visualize the cracks within alloys or walls. In medical fields, it has been used as 3D scanner to reconstruct some human organs such as internal nose for plastic surgery or to reconstruct ear canal for fabricating a hearing aid device, and others. These applications need high accuracy details and measurement that represent the main issue which should be taken in consideration, also the other issues are cost, movability, and ease of use which should be taken into consideration. This work has presented an approach for design and construc

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